Mercurial > repos > devteam > ncbi_blast_plus
changeset 11:4c4a0da938ff draft
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
Supports $GALAXY_SLOTS.
Includes more tests and heavy use of macros.
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_arabidopsis.extended.tabular Thu Dec 05 06:55:59 2013 -0500 @@ -0,0 +1,1 @@ +chunk_of_plant chrIII 100.00 630 0 0 1 630 4341 4970 0.0 1164 chrIII 630 630 630 0 100.00 1 1 GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT 630 23459830 gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_arabidopsis.standard.tabular Thu Dec 05 06:55:59 2013 -0500 @@ -0,0 +1,1 @@ +chunk_of_plant chrIII 100.00 630 0 0 1 630 4341 4970 0.0 1164
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_arabidopsis.xml Thu Dec 05 06:55:59 2013 -0500 @@ -0,0 +1,71 @@ +<?xml version="1.0"?> +<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> +<BlastOutput> + <BlastOutput_program>blastn</BlastOutput_program> + <BlastOutput_version>BLASTN 2.2.28+</BlastOutput_version> + <BlastOutput_reference>Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14.</BlastOutput_reference> + <BlastOutput_db>/mnt/galaxy/galaxy-central/database/files/000/dataset_857_files/blastdb</BlastOutput_db> + <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> + <BlastOutput_query-def>chunk_of_plant</BlastOutput_query-def> + <BlastOutput_query-len>630</BlastOutput_query-len> + <BlastOutput_param> + <Parameters> + <Parameters_expect>0.001</Parameters_expect> + <Parameters_sc-match>1</Parameters_sc-match> + <Parameters_sc-mismatch>-2</Parameters_sc-mismatch> + <Parameters_gap-open>0</Parameters_gap-open> + <Parameters_gap-extend>0</Parameters_gap-extend> + <Parameters_filter>L;m;</Parameters_filter> + </Parameters> + </BlastOutput_param> +<BlastOutput_iterations> +<Iteration> + <Iteration_iter-num>1</Iteration_iter-num> + <Iteration_query-ID>Query_1</Iteration_query-ID> + <Iteration_query-def>chunk_of_plant</Iteration_query-def> + <Iteration_query-len>630</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>gnl|BL_ORD_ID|2</Hit_id> + <Hit_def>chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence</Hit_def> + <Hit_accession>2</Hit_accession> + <Hit_len>23459830</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>1164.51</Hsp_bit-score> + <Hsp_score>630</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>630</Hsp_query-to> + <Hsp_hit-from>4341</Hsp_hit-from> + <Hsp_hit-to>4970</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>630</Hsp_identity> + <Hsp_positive>630</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>630</Hsp_align-len> + <Hsp_qseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_qseq> + <Hsp_hseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_hseq> + <Hsp_midline>||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>5</Statistics_db-num> + <Statistics_db-len>119146348</Statistics_db-len> + <Statistics_hsp-len>26</Statistics_hsp-len> + <Statistics_eff-space>71964315672</Statistics_eff-space> + <Statistics_kappa>0.46</Statistics_kappa> + <Statistics_lambda>1.28</Statistics_lambda> + <Statistics_entropy>0.85</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +</BlastOutput_iterations> +</BlastOutput> +
--- a/test-data/blastn_rhodopsin_vs_three_human.tabular Mon Sep 23 06:14:13 2013 -0400 +++ b/test-data/blastn_rhodopsin_vs_three_human.tabular Thu Dec 05 06:55:59 2013 -0500 @@ -1,7 +1,7 @@ -gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 92.10 1050 77 6 1 1047 88 1134 0.0 1474 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 92.07 1047 83 0 1 1047 88 1134 0.0 1474 gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.59 333 28 0 1 333 118 450 9e-133 460 gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.36 243 19 2 3127 3368 782 1023 7e-94 331 gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 94.22 173 10 0 1410 1582 448 620 8e-74 265 -gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.98 171 10 2 2854 3023 615 784 8e-69 248 -gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.58 962 75 6 1 959 118 1076 0.0 1323 -gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 87.55 1052 121 10 1 1047 88 1134 0.0 1208 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.94 170 12 0 2854 3023 615 784 8e-69 248 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.55 959 81 0 1 959 118 1076 0.0 1323 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 87.50 1048 129 2 1 1047 88 1134 0.0 1208
--- a/test-data/blastp_four_human_vs_rhodopsin.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Thu Dec 05 06:55:59 2013 -0500 @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastp</BlastOutput_program> - <BlastOutput_version>BLASTP 2.2.26+</BlastOutput_version> + <BlastOutput_version>BLASTP 2.2.28+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>sp|Q9BS26|ERP44_HUMAN</BlastOutput_query-ID> @@ -17,630 +17,649 @@ <Parameters_filter>F</Parameters_filter> </Parameters> </BlastOutput_param> - <BlastOutput_iterations> - <Iteration> - <Iteration_iter-num>1</Iteration_iter-num> - <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> - <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>406</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>30</Statistics_hsp-len> - <Statistics_eff-space>119568</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>2</Iteration_iter-num> - <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> - <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>406</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>30</Statistics_hsp-len> - <Statistics_eff-space>119568</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>3</Iteration_iter-num> - <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> - <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>406</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>30</Statistics_hsp-len> - <Statistics_eff-space>119568</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>4</Iteration_iter-num> - <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> - <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>406</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>30</Statistics_hsp-len> - <Statistics_eff-space>119568</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>5</Iteration_iter-num> - <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> - <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>406</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>30</Statistics_hsp-len> - <Statistics_eff-space>119568</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>6</Iteration_iter-num> - <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> - <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>406</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>30</Statistics_hsp-len> - <Statistics_eff-space>119568</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>7</Iteration_iter-num> - <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID> - <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> - <Iteration_query-len>1161</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>38</Statistics_hsp-len> - <Statistics_eff-space>348130</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>8</Iteration_iter-num> - <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID> - <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> - <Iteration_query-len>1161</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>38</Statistics_hsp-len> - <Statistics_eff-space>348130</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>9</Iteration_iter-num> - <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID> - <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> - <Iteration_query-len>1161</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>38</Statistics_hsp-len> - <Statistics_eff-space>348130</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>10</Iteration_iter-num> - <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID> - <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> - <Iteration_query-len>1161</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>38</Statistics_hsp-len> - <Statistics_eff-space>348130</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>11</Iteration_iter-num> - <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID> - <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> - <Iteration_query-len>1161</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>38</Statistics_hsp-len> - <Statistics_eff-space>348130</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>12</Iteration_iter-num> - <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID> - <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> - <Iteration_query-len>1161</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>38</Statistics_hsp-len> - <Statistics_eff-space>348130</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>13</Iteration_iter-num> - <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID> - <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> - <Iteration_query-len>1382</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>39</Statistics_hsp-len> - <Statistics_eff-space>414987</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>14</Iteration_iter-num> - <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID> - <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> - <Iteration_query-len>1382</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>39</Statistics_hsp-len> - <Statistics_eff-space>414987</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>15</Iteration_iter-num> - <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID> - <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> - <Iteration_query-len>1382</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>39</Statistics_hsp-len> - <Statistics_eff-space>414987</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>16</Iteration_iter-num> - <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID> - <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> - <Iteration_query-len>1382</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>39</Statistics_hsp-len> - <Statistics_eff-space>414987</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>17</Iteration_iter-num> - <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID> - <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> - <Iteration_query-len>1382</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>39</Statistics_hsp-len> - <Statistics_eff-space>414987</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>18</Iteration_iter-num> - <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID> - <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> - <Iteration_query-len>1382</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>39</Statistics_hsp-len> - <Statistics_eff-space>414987</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>19</Iteration_iter-num> - <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID> - <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>348</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>gi|57163783|ref|NP_001009242.1|</Hit_id> - <Hit_def>rhodopsin [Felis catus]</Hit_def> - <Hit_accession>NP_001009242</Hit_accession> - <Hit_len>348</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>701.049</Hsp_bit-score> - <Hsp_score>1808</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>1</Hsp_query-from> - <Hsp_query-to>348</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>348</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>336</Hsp_identity> - <Hsp_positive>343</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>348</Hsp_align-len> - <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq> - <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA</Hsp_hseq> - <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>101761</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>20</Iteration_iter-num> - <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID> - <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>348</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id> - <Hit_def>RecName: Full=Rhodopsin</Hit_def> - <Hit_accession>P56514</Hit_accession> - <Hit_len>354</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>619.002</Hsp_bit-score> - <Hsp_score>1595</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>1</Hsp_query-from> - <Hsp_query-to>341</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>342</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>290</Hsp_identity> - <Hsp_positive>322</Hsp_positive> - <Hsp_gaps>1</Hsp_gaps> - <Hsp_align-len>342</Hsp_align-len> - <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE</Hsp_qseq> - <Hsp_hseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE</Hsp_hseq> - <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA SKTE</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>101761</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>21</Iteration_iter-num> - <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID> - <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>348</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>gi|283855846|gb|ADB45242.1|</Hit_id> - <Hit_def>rhodopsin [Cynopterus brachyotis]</Hit_def> - <Hit_accession>ADB45242</Hit_accession> - <Hit_len>328</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>653.284</Hsp_bit-score> - <Hsp_score>1684</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>11</Hsp_query-from> - <Hsp_query-to>338</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>328</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>311</Hsp_identity> - <Hsp_positive>321</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>328</Hsp_align-len> - <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS</Hsp_qseq> - <Hsp_hseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS</Hsp_hseq> - <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>101761</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>22</Iteration_iter-num> - <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID> - <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>348</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>gi|283855823|gb|ADB45229.1|</Hit_id> - <Hit_def>rhodopsin [Myotis pilosus]</Hit_def> - <Hit_accession>ADB45229</Hit_accession> - <Hit_len>328</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>631.328</Hsp_bit-score> - <Hsp_score>1627</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>11</Hsp_query-from> - <Hsp_query-to>338</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>328</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>311</Hsp_identity> - <Hsp_positive>323</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>328</Hsp_align-len> - <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS</Hsp_qseq> - <Hsp_hseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS</Hsp_hseq> - <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>101761</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>23</Iteration_iter-num> - <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID> - <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>348</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>gi|223523|prf||0811197A</Hit_id> - <Hit_def>rhodopsin [Bos taurus]</Hit_def> - <Hit_accession>0811197A</Hit_accession> - <Hit_len>347</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>673.315</Hsp_bit-score> - <Hsp_score>1736</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>1</Hsp_query-from> - <Hsp_query-to>348</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>347</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>324</Hsp_identity> - <Hsp_positive>336</Hsp_positive> - <Hsp_gaps>1</Hsp_gaps> - <Hsp_align-len>348</Hsp_align-len> - <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq> - <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq> - <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>101761</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>24</Iteration_iter-num> - <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID> - <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>348</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>gi|12583665|dbj|BAB21486.1|</Hit_id> - <Hit_def>fresh water form rod opsin [Conger myriaster]</Hit_def> - <Hit_accession>BAB21486</Hit_accession> - <Hit_len>354</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>599.356</Hsp_bit-score> - <Hsp_score>1544</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>1</Hsp_query-from> - <Hsp_query-to>341</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>342</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>281</Hsp_identity> - <Hsp_positive>314</Hsp_positive> - <Hsp_gaps>1</Hsp_gaps> - <Hsp_align-len>342</Hsp_align-len> - <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq> - <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq> - <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +D ASAT SKTE</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>101761</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - </BlastOutput_iterations> -</BlastOutput> \ No newline at end of file +<BlastOutput_iterations> +<Iteration> + <Iteration_iter-num>1</Iteration_iter-num> + <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> + <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>406</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119568</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>2</Iteration_iter-num> + <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> + <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>406</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119568</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>3</Iteration_iter-num> + <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> + <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>406</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119568</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>4</Iteration_iter-num> + <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> + <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>406</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119568</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>5</Iteration_iter-num> + <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> + <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>406</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119568</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>6</Iteration_iter-num> + <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> + <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>406</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119568</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>7</Iteration_iter-num> + <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID> + <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> + <Iteration_query-len>1161</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>38</Statistics_hsp-len> + <Statistics_eff-space>348130</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>8</Iteration_iter-num> + <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID> + <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> + <Iteration_query-len>1161</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>38</Statistics_hsp-len> + <Statistics_eff-space>348130</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>9</Iteration_iter-num> + <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID> + <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> + <Iteration_query-len>1161</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>38</Statistics_hsp-len> + <Statistics_eff-space>348130</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>10</Iteration_iter-num> + <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID> + <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> + <Iteration_query-len>1161</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>38</Statistics_hsp-len> + <Statistics_eff-space>348130</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>11</Iteration_iter-num> + <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID> + <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> + <Iteration_query-len>1161</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>38</Statistics_hsp-len> + <Statistics_eff-space>348130</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>12</Iteration_iter-num> + <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID> + <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> + <Iteration_query-len>1161</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>38</Statistics_hsp-len> + <Statistics_eff-space>348130</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>13</Iteration_iter-num> + <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID> + <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> + <Iteration_query-len>1382</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>39</Statistics_hsp-len> + <Statistics_eff-space>414987</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>14</Iteration_iter-num> + <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID> + <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> + <Iteration_query-len>1382</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>39</Statistics_hsp-len> + <Statistics_eff-space>414987</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>15</Iteration_iter-num> + <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID> + <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> + <Iteration_query-len>1382</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>39</Statistics_hsp-len> + <Statistics_eff-space>414987</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>16</Iteration_iter-num> + <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID> + <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> + <Iteration_query-len>1382</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>39</Statistics_hsp-len> + <Statistics_eff-space>414987</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>17</Iteration_iter-num> + <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID> + <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> + <Iteration_query-len>1382</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>39</Statistics_hsp-len> + <Statistics_eff-space>414987</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>18</Iteration_iter-num> + <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID> + <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> + <Iteration_query-len>1382</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>39</Statistics_hsp-len> + <Statistics_eff-space>414987</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>19</Iteration_iter-num> + <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID> + <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>348</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>gi|57163783|ref|NP_001009242.1|</Hit_id> + <Hit_def>rhodopsin [Felis catus]</Hit_def> + <Hit_accession>NP_001009242</Hit_accession> + <Hit_len>348</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>701.049</Hsp_bit-score> + <Hsp_score>1808</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>348</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>348</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>336</Hsp_identity> + <Hsp_positive>343</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>348</Hsp_align-len> + <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq> + <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA</Hsp_hseq> + <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>29</Statistics_hsp-len> + <Statistics_eff-space>101761</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>20</Iteration_iter-num> + <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID> + <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>348</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id> + <Hit_def>RecName: Full=Rhodopsin</Hit_def> + <Hit_accession>P56514</Hit_accession> + <Hit_len>354</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>619.002</Hsp_bit-score> + <Hsp_score>1595</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>341</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>342</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>290</Hsp_identity> + <Hsp_positive>322</Hsp_positive> + <Hsp_gaps>1</Hsp_gaps> + <Hsp_align-len>342</Hsp_align-len> + <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE</Hsp_qseq> + <Hsp_hseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE</Hsp_hseq> + <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA SKTE</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>29</Statistics_hsp-len> + <Statistics_eff-space>101761</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>21</Iteration_iter-num> + <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID> + <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>348</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>gi|283855846|gb|ADB45242.1|</Hit_id> + <Hit_def>rhodopsin [Cynopterus brachyotis]</Hit_def> + <Hit_accession>ADB45242</Hit_accession> + <Hit_len>328</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>653.284</Hsp_bit-score> + <Hsp_score>1684</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>11</Hsp_query-from> + <Hsp_query-to>338</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>328</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>311</Hsp_identity> + <Hsp_positive>321</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>328</Hsp_align-len> + <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS</Hsp_qseq> + <Hsp_hseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS</Hsp_hseq> + <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>29</Statistics_hsp-len> + <Statistics_eff-space>101761</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>22</Iteration_iter-num> + <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID> + <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>348</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>gi|283855823|gb|ADB45229.1|</Hit_id> + <Hit_def>rhodopsin [Myotis pilosus]</Hit_def> + <Hit_accession>ADB45229</Hit_accession> + <Hit_len>328</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>631.328</Hsp_bit-score> + <Hsp_score>1627</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>11</Hsp_query-from> + <Hsp_query-to>338</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>328</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>311</Hsp_identity> + <Hsp_positive>323</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>328</Hsp_align-len> + <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS</Hsp_qseq> + <Hsp_hseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS</Hsp_hseq> + <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>29</Statistics_hsp-len> + <Statistics_eff-space>101761</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>23</Iteration_iter-num> + <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID> + <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>348</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>gi|223523|prf||0811197A</Hit_id> + <Hit_def>rhodopsin [Bos taurus]</Hit_def> + <Hit_accession>0811197A</Hit_accession> + <Hit_len>347</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>673.315</Hsp_bit-score> + <Hsp_score>1736</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>348</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>347</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>324</Hsp_identity> + <Hsp_positive>336</Hsp_positive> + <Hsp_gaps>1</Hsp_gaps> + <Hsp_align-len>348</Hsp_align-len> + <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq> + <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq> + <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>29</Statistics_hsp-len> + <Statistics_eff-space>101761</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>24</Iteration_iter-num> + <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID> + <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>348</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>gi|12583665|dbj|BAB21486.1|</Hit_id> + <Hit_def>fresh water form rod opsin [Conger myriaster]</Hit_def> + <Hit_accession>BAB21486</Hit_accession> + <Hit_len>354</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>599.356</Hsp_bit-score> + <Hsp_score>1544</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>341</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>342</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>281</Hsp_identity> + <Hsp_positive>314</Hsp_positive> + <Hsp_gaps>1</Hsp_gaps> + <Hsp_align-len>342</Hsp_align-len> + <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq> + <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq> + <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +D ASAT SKTE</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>29</Statistics_hsp-len> + <Statistics_eff-space>101761</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +</BlastOutput_iterations> +</BlastOutput> +
--- a/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Mon Sep 23 06:14:13 2013 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Thu Dec 05 06:55:59 2013 -0500 @@ -1,6 +1,6 @@ -sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 701 gi|57163783|ref|NP_001009242.1| 1808 336 343 0 98.56 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 348 -sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 0.0 619 gi|3024260|sp|P56514.1|OPSD_BUFBU 1595 290 322 1 94.15 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 354 -sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0 653 gi|283855846|gb|ADB45242.1| 1684 311 321 0 97.87 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 -sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0 631 gi|283855823|gb|ADB45229.1| 1627 311 323 0 98.48 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 -sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 673 gi|223523|prf||0811197A 1736 324 336 1 96.55 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 347 -sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0 599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354 +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 701 gi|57163783|ref|NP_001009242.1| 1808 336 343 0 98.56 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 348 rhodopsin [Felis catus] +sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 0.0 619 gi|3024260|sp|P56514.1|OPSD_BUFBU 1595 290 322 1 94.15 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 354 RecName: Full=Rhodopsin +sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0 653 gi|283855846|gb|ADB45242.1| 1684 311 321 0 97.87 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 rhodopsin [Cynopterus brachyotis] +sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0 631 gi|283855823|gb|ADB45229.1| 1627 311 323 0 98.48 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 rhodopsin [Myotis pilosus] +sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 673 gi|223523|prf||0811197A 1736 324 336 1 96.55 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 347 rhodopsin [Bos taurus] +sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0 599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354 fresh water form rod opsin [Conger myriaster]
--- a/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Mon Sep 23 06:14:13 2013 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Thu Dec 05 06:55:59 2013 -0500 @@ -1,6 +1,6 @@ -sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 701 gi|57163783|ref|NP_001009242.1| 1808 336 343 0 98.56 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 348 -sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 0.0 619 gi|3024260|sp|P56514.1|OPSD_BUFBU 1595 290 322 1 94.15 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 354 -sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0 653 gi|283855846|gb|ADB45242.1| 1684 311 321 0 97.87 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 -sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0 631 gi|283855823|gb|ADB45229.1| 1627 311 323 0 98.48 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 -sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 673 gi|223523|prf||0811197A 1736 324 336 1 96.55 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 347 -sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0 599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354 +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 701 gi|57163783|ref|NP_001009242.1| 1808 336 343 0 98.56 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 348 N/A +sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 0.0 619 gi|3024260|sp|P56514.1|OPSD_BUFBU 1595 290 322 1 94.15 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 354 N/A +sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0 653 gi|283855846|gb|ADB45242.1| 1684 311 321 0 97.87 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 N/A +sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0 631 gi|283855823|gb|ADB45229.1| 1627 311 323 0 98.48 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 N/A +sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 673 gi|223523|prf||0811197A 1736 324 336 1 96.55 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 347 N/A +sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0 599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354 N/A
--- a/test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular Mon Sep 23 06:14:13 2013 -0400 +++ b/test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular Thu Dec 05 06:55:59 2013 -0500 @@ -1,8 +1,8 @@ -sp|Q9BS26|ERP44_HUMAN gi|193885198|pdb|2R2J|A 97.11 381 11 0 26 406 2 382 0.0 768 gi|193885198|pdb|2R2J|A 1982 370 372 0 97.64 1 1 PVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL PLGSEITSLDTENIDEILNNADVALVNFYADWCRFSQXLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGXXXKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDXVYLGAXTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHXKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHXYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL 406 382 -sp|Q9BS26|ERP44_HUMAN gi|88192228|pdb|2B5E|A 25.17 290 193 8 25 306 10 283 4e-20 95.1 gi|88192228|pdb|2B5E|A;gi|206581884|pdb|3BOA|A 235 73 133 24 45.86 1 1 TPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKR-EYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNI---IYKPPGHSAPDMVYLGA---MTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKF-RH APEDSAVVKLATDSFNEYIQSHDLVLAEFFAPWCGHCKNMAPEYVKAAETLVEK-----NITLAQIDCTENQDLCMEHNIPGFPSLKIFKNSDVNNSIDYEGPRTAEAIVQFMIKQSQPAVAVVADLPAYLANETFVTPVIVQSGKIDADFNATFYSMANKHFNDYDFVSA--------ENADDDFKLSIYLPSAMDEP-VVYNGKKADIADADVFEKWLQVEALPYFGEIDGSVFAQYVESGLPLGYLFY--NDEEELEEYKPLFTELAKKNRGLMNFVSIDARKFGRH 406 504 -sp|Q9NSY1|BMP2K_HUMAN gi|73536291|pdb|2BUJ|A 29.39 279 182 8 40 308 21 294 1e-22 105 gi|73536291|pdb|2BUJ|A;gi|73536292|pdb|2BUJ|B 262 82 130 15 46.59 1 1 GVRVFAVGRHQVTLEESLAEGGFSTVFLVR-THGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTG--FTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDG-VNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPF------GESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDI GHMVIIDNKHYLFIQK-LGEGGFSYVDLVEGLHDGHFYALKRILCHEQQDREEAQREAD-MHRLFNHPNILRLVAYCLRERGAKH-EAWLLLPFFKRGTLWNEIERLKDKGNFLTEDQILWLLLGICRGLEAIH--AKGYAHRDLKPTNILLGDEGQPVLMDLGSMNQACIHVEGSRQALTLQDWAAQRCTISYRAPELFSVQSHCVIDERTDVWSLGCVLYAMMFGEGPYDMVFQKGDSVALAVQNQLSIPQSPRHSSALWQLLNSMMTVDPHQRPHI 1161 317 -sp|Q9NSY1|BMP2K_HUMAN gi|270346335|pdb|2WQM|A 27.21 272 166 12 53 311 36 288 6e-17 86.3 gi|270346335|pdb|2WQM|A;gi|270346336|pdb|2WQN|A 212 74 129 32 47.43 1 1 LEESLAEGGFSTVFLVRTH-GGIRCALKRMYVNNMPDLNV---CKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMN--KKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPFGESQV---AICD----GNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQV IEKKIGRGQFSEVYRAACLLDGVPVALKKVQIFDLMDAKARADCIKEIDLLKQLN-HPNVIKYY---ASFIEDN--ELNIVLELADAGDLSRMIKHFKKQKRLIPERTVWKYFVQLCSALEHMHSRR--VMHRDIKPANVFITATGVVKLGDLG--LGRFFSSKTTAAHSL------VGTPYYMSPERIHENG---YNFKSDIWSLGCLLYEMAALQSPFYGDKMNLYSLCKKIEQCDYPPLPSDHYSEELRQLVNMCINPDPEKRPDVTYV 1161 310 -sp|P06213|INSR_HUMAN gi|116667097|pdb|2DTG|E 95.91 928 7 2 28 955 1 897 0.0 1846 gi|116667097|pdb|2DTG|E 4781 890 893 31 96.23 1 1 HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCVSRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFV------------PRPSRKRRSLGDVGNA-------------------GNNEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCDTRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA 1382 897 -sp|P06213|INSR_HUMAN gi|114794482|pdb|2HR7|A 99.59 485 2 0 28 512 1 485 0.0 1016 gi|114794482|pdb|2HR7|A;gi|114794483|pdb|2HR7|B 2628 483 485 0 100.00 1 1 HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKI HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDKASCENELLKFSYIRTSFDKI 1382 486 -sp|P08100|OPSD_HUMAN gi|16975387|pdb|1JFP|A 93.39 348 23 0 1 348 1 348 0.0 681 gi|16975387|pdb|1JFP|A;gi|22219255|pdb|1LN6|A;gi|157878065|pdb|1GZM|A;gi|157878066|pdb|1GZM|B;gi|157878298|pdb|1HZX|A;gi|157878299|pdb|1HZX|B;gi|157878979|pdb|1L9H|A;gi|157878980|pdb|1L9H|B;gi|157880263|pdb|1U19|A;gi|157880264|pdb|1U19|B;gi|157883606|pdb|2G87|A;gi|157883607|pdb|2G87|B;gi|157883830|pdb|2HPY|A;gi|157883831|pdb|2HPY|B;gi|157883860|pdb|2I35|A;gi|157883861|pdb|2I36|A;gi|157883862|pdb|2I36|B;gi|157883863|pdb|2I36|C;gi|157883864|pdb|2I37|A;gi|157883865|pdb|2I37|B;gi|157883866|pdb|2I37|C;gi|159795066|pdb|2PED|A;gi|159795067|pdb|2PED|B;gi|192988480|pdb|3CAP|A;gi|192988481|pdb|3CAP|B;gi|195927457|pdb|3C9L|A;gi|197107530|pdb|1F88|A;gi|197107531|pdb|1F88|B;gi|206582030|pdb|3DQB|A 1756 325 337 0 96.84 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 348 -sp|P08100|OPSD_HUMAN gi|195927458|pdb|3C9M|A 93.10 348 24 0 1 348 1 348 0.0 674 gi|195927458|pdb|3C9M|A 1738 324 335 0 96.26 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 348 +sp|Q9BS26|ERP44_HUMAN gi|193885198|pdb|2R2J|A 97.11 381 11 0 26 406 2 382 0.0 768 gi|193885198|pdb|2R2J|A 1982 370 372 0 97.64 1 1 PVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL PLGSEITSLDTENIDEILNNADVALVNFYADWCRFSQXLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGXXXKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDXVYLGAXTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHXKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHXYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL 406 382 Chain A, Crystal Structure Of Human Erp44 +sp|Q9BS26|ERP44_HUMAN gi|88192228|pdb|2B5E|A 25.17 290 193 8 25 306 10 283 4e-20 95.1 gi|88192228|pdb|2B5E|A;gi|206581884|pdb|3BOA|A 235 73 133 24 45.86 1 1 TPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKR-EYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNI---IYKPPGHSAPDMVYLGA---MTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKF-RH APEDSAVVKLATDSFNEYIQSHDLVLAEFFAPWCGHCKNMAPEYVKAAETLVEK-----NITLAQIDCTENQDLCMEHNIPGFPSLKIFKNSDVNNSIDYEGPRTAEAIVQFMIKQSQPAVAVVADLPAYLANETFVTPVIVQSGKIDADFNATFYSMANKHFNDYDFVSA--------ENADDDFKLSIYLPSAMDEP-VVYNGKKADIADADVFEKWLQVEALPYFGEIDGSVFAQYVESGLPLGYLFY--NDEEELEEYKPLFTELAKKNRGLMNFVSIDARKFGRH 406 504 Chain A, Crystal Structure Of Yeast Protein Disulfide Isomerase<>Chain A, Crystal Structure Of Yeast Protein Disulfide Isomerase. +sp|Q9NSY1|BMP2K_HUMAN gi|73536291|pdb|2BUJ|A 29.39 279 182 8 40 308 21 294 1e-22 105 gi|73536291|pdb|2BUJ|A;gi|73536292|pdb|2BUJ|B 262 82 130 15 46.59 1 1 GVRVFAVGRHQVTLEESLAEGGFSTVFLVR-THGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTG--FTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDG-VNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPF------GESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDI GHMVIIDNKHYLFIQK-LGEGGFSYVDLVEGLHDGHFYALKRILCHEQQDREEAQREAD-MHRLFNHPNILRLVAYCLRERGAKH-EAWLLLPFFKRGTLWNEIERLKDKGNFLTEDQILWLLLGICRGLEAIH--AKGYAHRDLKPTNILLGDEGQPVLMDLGSMNQACIHVEGSRQALTLQDWAAQRCTISYRAPELFSVQSHCVIDERTDVWSLGCVLYAMMFGEGPYDMVFQKGDSVALAVQNQLSIPQSPRHSSALWQLLNSMMTVDPHQRPHI 1161 317 Chain A, Crystal Structure Of The Human Serine-Threonine Kinase 16 In Complex With Staurosporine<>Chain B, Crystal Structure Of The Human Serine-Threonine Kinase 16 In Complex With Staurosporine +sp|Q9NSY1|BMP2K_HUMAN gi|270346335|pdb|2WQM|A 27.21 272 166 12 53 311 36 288 6e-17 86.3 gi|270346335|pdb|2WQM|A;gi|270346336|pdb|2WQN|A 212 74 129 32 47.43 1 1 LEESLAEGGFSTVFLVRTH-GGIRCALKRMYVNNMPDLNV---CKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMN--KKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPFGESQV---AICD----GNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQV IEKKIGRGQFSEVYRAACLLDGVPVALKKVQIFDLMDAKARADCIKEIDLLKQLN-HPNVIKYY---ASFIEDN--ELNIVLELADAGDLSRMIKHFKKQKRLIPERTVWKYFVQLCSALEHMHSRR--VMHRDIKPANVFITATGVVKLGDLG--LGRFFSSKTTAAHSL------VGTPYYMSPERIHENG---YNFKSDIWSLGCLLYEMAALQSPFYGDKMNLYSLCKKIEQCDYPPLPSDHYSEELRQLVNMCINPDPEKRPDVTYV 1161 310 Chain A, Structure Of Apo Human Nek7<>Chain A, Structure Of Adp-Bound Human Nek7 +sp|P06213|INSR_HUMAN gi|116667097|pdb|2DTG|E 95.91 928 7 2 28 955 1 897 0.0 1846 gi|116667097|pdb|2DTG|E 4781 890 893 31 96.23 1 1 HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCVSRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFV------------PRPSRKRRSLGDVGNA-------------------GNNEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCDTRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA 1382 897 Chain E, Insulin Receptor (Ir) Ectodomain In Complex With Fab's +sp|P06213|INSR_HUMAN gi|114794482|pdb|2HR7|A 99.59 485 2 0 28 512 1 485 0.0 1016 gi|114794482|pdb|2HR7|A;gi|114794483|pdb|2HR7|B 2628 483 485 0 100.00 1 1 HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKI HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDKASCENELLKFSYIRTSFDKI 1382 486 Chain A, Insulin Receptor (Domains 1-3)<>Chain B, Insulin Receptor (Domains 1-3) +sp|P08100|OPSD_HUMAN gi|16975387|pdb|1JFP|A 93.39 348 23 0 1 348 1 348 0.0 681 gi|16975387|pdb|1JFP|A;gi|22219255|pdb|1LN6|A;gi|157878065|pdb|1GZM|A;gi|157878066|pdb|1GZM|B;gi|157878298|pdb|1HZX|A;gi|157878299|pdb|1HZX|B;gi|157878979|pdb|1L9H|A;gi|157878980|pdb|1L9H|B;gi|157880263|pdb|1U19|A;gi|157880264|pdb|1U19|B;gi|157883606|pdb|2G87|A;gi|157883607|pdb|2G87|B;gi|157883830|pdb|2HPY|A;gi|157883831|pdb|2HPY|B;gi|157883860|pdb|2I35|A;gi|157883861|pdb|2I36|A;gi|157883862|pdb|2I36|B;gi|157883863|pdb|2I36|C;gi|157883864|pdb|2I37|A;gi|157883865|pdb|2I37|B;gi|157883866|pdb|2I37|C;gi|159795066|pdb|2PED|A;gi|159795067|pdb|2PED|B;gi|192988480|pdb|3CAP|A;gi|192988481|pdb|3CAP|B;gi|195927457|pdb|3C9L|A;gi|197107530|pdb|1F88|A;gi|197107531|pdb|1F88|B;gi|206582030|pdb|3DQB|A 1756 325 337 0 96.84 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 348 Chain A, Structure Of Bovine Rhodopsin (Dark Adapted)<>Chain A, Structure Of Bovine Rhodopsin (Metarhodopsin Ii)<>Chain A, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form<>Chain B, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form<>Chain A, Crystal Structure Of Bovine Rhodopsin<>Chain B, Crystal Structure Of Bovine Rhodopsin<>Chain A, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms Resolution<>Chain B, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms Resolution<>Chain A, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms Resolution<>Chain B, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms Resolution<>Chain A, Crystallographic Model Of Bathorhodopsin<>Chain B, Crystallographic Model Of Bathorhodopsin<>Chain A, Crystallographic Model Of Lumirhodopsin<>Chain B, Crystallographic Model Of Lumirhodopsin<>Chain A, Crystal Structure Of Rhombohedral Crystal Form Of Ground- State Rhodopsin<>Chain A, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin<>Chain B, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin<>Chain C, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin<>Chain A, Crystal Structure Of A Photoactivated Rhodopsin<>Chain B, Crystal Structure Of A Photoactivated Rhodopsin<>Chain C, Crystal Structure Of A Photoactivated Rhodopsin<>Chain A, Crystallographic Model Of 9-Cis-Rhodopsin<>Chain B, Crystallographic Model Of 9-Cis-Rhodopsin<>Chain A, Crystal Structure Of Native Opsin: The G Protein-Coupled Receptor Rhodopsin In Its Ligand-Free State<>Chain B, Crystal Structure Of Native Opsin: The G Protein-Coupled Receptor Rhodopsin In Its Ligand-Free State<>Chain A, Structure Of Ground-State Bovine Rhodospin In A Hexagonal Crystal Form<>Chain A, Crystal Structure Of Bovine Rhodopsin<>Chain B, Crystal Structure Of Bovine Rhodopsin<>Chain A, Crystal Structure Of The Active G-Protein-Coupled Receptor Opsin In Complex With A C-Terminal Peptide Derived From The Galpha Subunit Of Transducin +sp|P08100|OPSD_HUMAN gi|195927458|pdb|3C9M|A 93.10 348 24 0 1 348 1 348 0.0 674 gi|195927458|pdb|3C9M|A 1738 324 335 0 96.26 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 348 Chain A, Structure Of A Mutant Bovine Rhodopsin In Hexagonal Crystal Form
--- a/test-data/blastx_rhodopsin_vs_four_human.tabular Mon Sep 23 06:14:13 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human.tabular Thu Dec 05 06:55:59 2013 -0500 @@ -1,10 +1,10 @@ -gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 662 -gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 575 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-68 224 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-36 129 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 3e-33 120 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 2e-32 118 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 2e-12 56.2 -gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 613 -gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 641 -gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 0.0 559 +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532
--- a/test-data/blastx_rhodopsin_vs_four_human.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Thu Dec 05 06:55:59 2013 -0500 @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastx</BlastOutput_program> - <BlastOutput_version>BLASTX 2.2.26+</BlastOutput_version> + <BlastOutput_version>BLASTX 2.2.28+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> @@ -17,706 +17,725 @@ <Parameters_filter>L;</Parameters_filter> </Parameters> </BlastOutput_param> - <BlastOutput_iterations> - <Iteration> - <Iteration_iter-num>1</Iteration_iter-num> - <Iteration_query-ID>Query_1</Iteration_query-ID> - <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def> - <Iteration_query-len>1047</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>102080</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>2</Iteration_iter-num> - <Iteration_query-ID>Query_1</Iteration_query-ID> - <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def> - <Iteration_query-len>1047</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>102080</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>3</Iteration_iter-num> - <Iteration_query-ID>Query_1</Iteration_query-ID> - <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def> - <Iteration_query-len>1047</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>102080</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>4</Iteration_iter-num> - <Iteration_query-ID>Query_1</Iteration_query-ID> - <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def> - <Iteration_query-len>1047</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>Subject_4</Hit_id> - <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def> - <Hit_accession>Subject_4</Hit_accession> - <Hit_len>348</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>662.144</Hsp_bit-score> - <Hsp_score>1707</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>1</Hsp_query-from> - <Hsp_query-to>1044</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>348</Hsp_hit-to> - <Hsp_query-frame>1</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>336</Hsp_identity> - <Hsp_positive>343</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>348</Hsp_align-len> - <Hsp_qseq>MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA</Hsp_qseq> - <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_hseq> - <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>102080</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>5</Iteration_iter-num> - <Iteration_query-ID>Query_2</Iteration_query-ID> - <Iteration_query-def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Iteration_query-def> - <Iteration_query-len>1574</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>32</Statistics_hsp-len> - <Statistics_eff-space>155472</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>6</Iteration_iter-num> - <Iteration_query-ID>Query_2</Iteration_query-ID> - <Iteration_query-def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Iteration_query-def> - <Iteration_query-len>1574</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>32</Statistics_hsp-len> - <Statistics_eff-space>155472</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>7</Iteration_iter-num> - <Iteration_query-ID>Query_2</Iteration_query-ID> - <Iteration_query-def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Iteration_query-def> - <Iteration_query-len>1574</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>32</Statistics_hsp-len> - <Statistics_eff-space>155472</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>8</Iteration_iter-num> - <Iteration_query-ID>Query_2</Iteration_query-ID> - <Iteration_query-def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Iteration_query-def> - <Iteration_query-len>1574</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>Subject_4</Hit_id> - <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def> - <Hit_accession>Subject_4</Hit_accession> - <Hit_len>348</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>575.089</Hsp_bit-score> - <Hsp_score>1481</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>42</Hsp_query-from> - <Hsp_query-to>1037</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>332</Hsp_hit-to> - <Hsp_query-frame>3</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>283</Hsp_identity> - <Hsp_positive>315</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>332</Hsp_align-len> - <Hsp_qseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD</Hsp_qseq> - <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE</Hsp_hseq> - <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>32</Statistics_hsp-len> - <Statistics_eff-space>155472</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>9</Iteration_iter-num> - <Iteration_query-ID>Query_3</Iteration_query-ID> - <Iteration_query-def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Iteration_query-def> - <Iteration_query-len>4301</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>39</Statistics_hsp-len> - <Statistics_eff-space>430746</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>10</Iteration_iter-num> - <Iteration_query-ID>Query_3</Iteration_query-ID> - <Iteration_query-def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Iteration_query-def> - <Iteration_query-len>4301</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>39</Statistics_hsp-len> - <Statistics_eff-space>430746</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>11</Iteration_iter-num> - <Iteration_query-ID>Query_3</Iteration_query-ID> - <Iteration_query-def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Iteration_query-def> - <Iteration_query-len>4301</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>39</Statistics_hsp-len> - <Statistics_eff-space>430746</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>12</Iteration_iter-num> - <Iteration_query-ID>Query_3</Iteration_query-ID> - <Iteration_query-def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Iteration_query-def> - <Iteration_query-len>4301</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>Subject_4</Hit_id> - <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def> - <Hit_accession>Subject_4</Hit_accession> - <Hit_len>348</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>224.172</Hsp_bit-score> - <Hsp_score>570</Hsp_score> - <Hsp_evalue>1.84906e-68</Hsp_evalue> - <Hsp_query-from>1</Hsp_query-from> - <Hsp_query-to>333</Hsp_query-to> - <Hsp_hit-from>11</Hsp_hit-from> - <Hsp_hit-to>121</Hsp_hit-to> - <Hsp_query-frame>1</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>107</Hsp_identity> - <Hsp_positive>109</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>111</Hsp_align-len> - <Hsp_qseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_qseq> - <Hsp_hseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_hseq> - <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_midline> - </Hsp> - <Hsp> - <Hsp_num>2</Hsp_num> - <Hsp_bit-score>129.413</Hsp_bit-score> - <Hsp_score>324</Hsp_score> - <Hsp_evalue>4.62305e-36</Hsp_evalue> - <Hsp_query-from>3174</Hsp_query-from> - <Hsp_query-to>3368</Hsp_query-to> - <Hsp_hit-from>248</Hsp_hit-from> - <Hsp_hit-to>312</Hsp_hit-to> - <Hsp_query-frame>3</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>60</Hsp_identity> - <Hsp_positive>64</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>65</Hsp_align-len> - <Hsp_qseq>KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ</Hsp_qseq> - <Hsp_hseq>KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ</Hsp_hseq> - <Hsp_midline>KEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ</Hsp_midline> - </Hsp> - <Hsp> - <Hsp_num>3</Hsp_num> - <Hsp_bit-score>120.939</Hsp_bit-score> - <Hsp_score>302</Hsp_score> - <Hsp_evalue>2.85192e-33</Hsp_evalue> - <Hsp_query-from>2855</Hsp_query-from> - <Hsp_query-to>3022</Hsp_query-to> - <Hsp_hit-from>177</Hsp_hit-from> - <Hsp_hit-to>232</Hsp_hit-to> - <Hsp_query-frame>2</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>54</Hsp_identity> - <Hsp_positive>56</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>56</Hsp_align-len> - <Hsp_qseq>RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE</Hsp_qseq> - <Hsp_hseq>RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE</Hsp_hseq> - <Hsp_midline>RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE</Hsp_midline> - </Hsp> - <Hsp> - <Hsp_num>4</Hsp_num> - <Hsp_bit-score>118.242</Hsp_bit-score> - <Hsp_score>295</Hsp_score> - <Hsp_evalue>2.16231e-32</Hsp_evalue> - <Hsp_query-from>1404</Hsp_query-from> - <Hsp_query-to>1580</Hsp_query-to> - <Hsp_hit-from>119</Hsp_hit-from> - <Hsp_hit-to>177</Hsp_hit-to> - <Hsp_query-frame>3</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>55</Hsp_identity> - <Hsp_positive>56</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>59</Hsp_align-len> - <Hsp_qseq>LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR</Hsp_qseq> - <Hsp_hseq>LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR</Hsp_hseq> - <Hsp_midline>L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR</Hsp_midline> - </Hsp> - <Hsp> - <Hsp_num>5</Hsp_num> - <Hsp_bit-score>56.225</Hsp_bit-score> - <Hsp_score>134</Hsp_score> - <Hsp_evalue>2.05678e-12</Hsp_evalue> - <Hsp_query-from>4222</Hsp_query-from> - <Hsp_query-to>4296</Hsp_query-to> - <Hsp_hit-from>312</Hsp_hit-from> - <Hsp_hit-to>336</Hsp_hit-to> - <Hsp_query-frame>1</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>23</Hsp_identity> - <Hsp_positive>24</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>25</Hsp_align-len> - <Hsp_qseq>QFRNCMLTTLCCGKNPLGDDEASTT</Hsp_qseq> - <Hsp_hseq>QFRNCMLTTICCGKNPLGDDEASAT</Hsp_hseq> - <Hsp_midline>QFRNCMLTT+CCGKNPLGDDEAS T</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>39</Statistics_hsp-len> - <Statistics_eff-space>430746</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>13</Iteration_iter-num> - <Iteration_query-ID>Query_4</Iteration_query-ID> - <Iteration_query-def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Iteration_query-def> - <Iteration_query-len>983</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>28</Statistics_hsp-len> - <Statistics_eff-space>95680</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>14</Iteration_iter-num> - <Iteration_query-ID>Query_4</Iteration_query-ID> - <Iteration_query-def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Iteration_query-def> - <Iteration_query-len>983</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>28</Statistics_hsp-len> - <Statistics_eff-space>95680</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>15</Iteration_iter-num> - <Iteration_query-ID>Query_4</Iteration_query-ID> - <Iteration_query-def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Iteration_query-def> - <Iteration_query-len>983</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>28</Statistics_hsp-len> - <Statistics_eff-space>95680</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>16</Iteration_iter-num> - <Iteration_query-ID>Query_4</Iteration_query-ID> - <Iteration_query-def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Iteration_query-def> - <Iteration_query-len>983</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>Subject_4</Hit_id> - <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def> - <Hit_accession>Subject_4</Hit_accession> - <Hit_len>348</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>613.994</Hsp_bit-score> - <Hsp_score>1582</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>1</Hsp_query-from> - <Hsp_query-to>978</Hsp_query-to> - <Hsp_hit-from>11</Hsp_hit-from> - <Hsp_hit-to>336</Hsp_hit-to> - <Hsp_query-frame>1</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>310</Hsp_identity> - <Hsp_positive>322</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>326</Hsp_align-len> - <Hsp_qseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT</Hsp_qseq> - <Hsp_hseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT</Hsp_hseq> - <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>28</Statistics_hsp-len> - <Statistics_eff-space>95680</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>17</Iteration_iter-num> - <Iteration_query-ID>Query_5</Iteration_query-ID> - <Iteration_query-def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Iteration_query-def> - <Iteration_query-len>1047</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>102080</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>18</Iteration_iter-num> - <Iteration_query-ID>Query_5</Iteration_query-ID> - <Iteration_query-def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Iteration_query-def> - <Iteration_query-len>1047</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>102080</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>19</Iteration_iter-num> - <Iteration_query-ID>Query_5</Iteration_query-ID> - <Iteration_query-def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Iteration_query-def> - <Iteration_query-len>1047</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>102080</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>20</Iteration_iter-num> - <Iteration_query-ID>Query_5</Iteration_query-ID> - <Iteration_query-def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Iteration_query-def> - <Iteration_query-len>1047</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>Subject_4</Hit_id> - <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def> - <Hit_accession>Subject_4</Hit_accession> - <Hit_len>348</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>641.728</Hsp_bit-score> - <Hsp_score>1654</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>1</Hsp_query-from> - <Hsp_query-to>1044</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>348</Hsp_hit-to> - <Hsp_query-frame>1</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>325</Hsp_identity> - <Hsp_positive>337</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>348</Hsp_align-len> - <Hsp_qseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_qseq> - <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_hseq> - <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>29</Statistics_hsp-len> - <Statistics_eff-space>102080</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>21</Iteration_iter-num> - <Iteration_query-ID>Query_6</Iteration_query-ID> - <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def> - <Iteration_query-len>1344</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>31</Statistics_hsp-len> - <Statistics_eff-space>132189</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>22</Iteration_iter-num> - <Iteration_query-ID>Query_6</Iteration_query-ID> - <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def> - <Iteration_query-len>1344</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>31</Statistics_hsp-len> - <Statistics_eff-space>132189</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>23</Iteration_iter-num> - <Iteration_query-ID>Query_6</Iteration_query-ID> - <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def> - <Iteration_query-len>1344</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>31</Statistics_hsp-len> - <Statistics_eff-space>132189</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>24</Iteration_iter-num> - <Iteration_query-ID>Query_6</Iteration_query-ID> - <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def> - <Iteration_query-len>1344</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>Subject_4</Hit_id> - <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def> - <Hit_accession>Subject_4</Hit_accession> - <Hit_len>348</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>559.296</Hsp_bit-score> - <Hsp_score>1440</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>23</Hsp_query-from> - <Hsp_query-to>1018</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>332</Hsp_hit-to> - <Hsp_query-frame>2</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>272</Hsp_identity> - <Hsp_positive>307</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>332</Hsp_align-len> - <Hsp_qseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED</Hsp_qseq> - <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE</Hsp_hseq> - <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +++</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>31</Statistics_hsp-len> - <Statistics_eff-space>132189</Statistics_eff-space> - <Statistics_kappa>0.041</Statistics_kappa> - <Statistics_lambda>0.267</Statistics_lambda> - <Statistics_entropy>0.14</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - </BlastOutput_iterations> -</BlastOutput> \ No newline at end of file +<BlastOutput_iterations> +<Iteration> + <Iteration_iter-num>1</Iteration_iter-num> + <Iteration_query-ID>Query_1</Iteration_query-ID> + <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def> + <Iteration_query-len>1047</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119944</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>2</Iteration_iter-num> + <Iteration_query-ID>Query_1</Iteration_query-ID> + <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def> + <Iteration_query-len>1047</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119944</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>3</Iteration_iter-num> + <Iteration_query-ID>Query_1</Iteration_query-ID> + <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def> + <Iteration_query-len>1047</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119944</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>4</Iteration_iter-num> + <Iteration_query-ID>Query_1</Iteration_query-ID> + <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def> + <Iteration_query-len>1047</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>Subject_4</Hit_id> + <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def> + <Hit_accession>Subject_4</Hit_accession> + <Hit_len>348</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>639.032</Hsp_bit-score> + <Hsp_score>1647</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>1044</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>348</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>336</Hsp_identity> + <Hsp_positive>343</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>348</Hsp_align-len> + <Hsp_qseq>MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA</Hsp_qseq> + <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_hseq> + <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119944</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>5</Iteration_iter-num> + <Iteration_query-ID>Query_2</Iteration_query-ID> + <Iteration_query-def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Iteration_query-def> + <Iteration_query-len>1574</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>33</Statistics_hsp-len> + <Statistics_eff-space>183143</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>6</Iteration_iter-num> + <Iteration_query-ID>Query_2</Iteration_query-ID> + <Iteration_query-def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Iteration_query-def> + <Iteration_query-len>1574</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>33</Statistics_hsp-len> + <Statistics_eff-space>183143</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>7</Iteration_iter-num> + <Iteration_query-ID>Query_2</Iteration_query-ID> + <Iteration_query-def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Iteration_query-def> + <Iteration_query-len>1574</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>33</Statistics_hsp-len> + <Statistics_eff-space>183143</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>8</Iteration_iter-num> + <Iteration_query-ID>Query_2</Iteration_query-ID> + <Iteration_query-def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Iteration_query-def> + <Iteration_query-len>1574</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>Subject_4</Hit_id> + <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def> + <Hit_accession>Subject_4</Hit_accession> + <Hit_len>348</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>551.206</Hsp_bit-score> + <Hsp_score>1419</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>42</Hsp_query-from> + <Hsp_query-to>1037</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>332</Hsp_hit-to> + <Hsp_query-frame>3</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>283</Hsp_identity> + <Hsp_positive>315</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>332</Hsp_align-len> + <Hsp_qseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD</Hsp_qseq> + <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE</Hsp_hseq> + <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>33</Statistics_hsp-len> + <Statistics_eff-space>183143</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>9</Iteration_iter-num> + <Iteration_query-ID>Query_3</Iteration_query-ID> + <Iteration_query-def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Iteration_query-def> + <Iteration_query-len>4301</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>40</Statistics_hsp-len> + <Statistics_eff-space>509838</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>10</Iteration_iter-num> + <Iteration_query-ID>Query_3</Iteration_query-ID> + <Iteration_query-def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Iteration_query-def> + <Iteration_query-len>4301</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>40</Statistics_hsp-len> + <Statistics_eff-space>509838</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>11</Iteration_iter-num> + <Iteration_query-ID>Query_3</Iteration_query-ID> + <Iteration_query-def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Iteration_query-def> + <Iteration_query-len>4301</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>40</Statistics_hsp-len> + <Statistics_eff-space>509838</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>12</Iteration_iter-num> + <Iteration_query-ID>Query_3</Iteration_query-ID> + <Iteration_query-def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Iteration_query-def> + <Iteration_query-len>4301</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>Subject_4</Hit_id> + <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def> + <Hit_accession>Subject_4</Hit_accession> + <Hit_len>348</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>220.32</Hsp_bit-score> + <Hsp_score>560</Hsp_score> + <Hsp_evalue>4.29169e-67</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>333</Hsp_query-to> + <Hsp_hit-from>11</Hsp_hit-from> + <Hsp_hit-to>121</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>107</Hsp_identity> + <Hsp_positive>109</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>111</Hsp_align-len> + <Hsp_qseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_qseq> + <Hsp_hseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_hseq> + <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>127.487</Hsp_bit-score> + <Hsp_score>319</Hsp_score> + <Hsp_evalue>1.95079e-35</Hsp_evalue> + <Hsp_query-from>3174</Hsp_query-from> + <Hsp_query-to>3368</Hsp_query-to> + <Hsp_hit-from>248</Hsp_hit-from> + <Hsp_hit-to>312</Hsp_hit-to> + <Hsp_query-frame>3</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>60</Hsp_identity> + <Hsp_positive>64</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>65</Hsp_align-len> + <Hsp_qseq>KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ</Hsp_qseq> + <Hsp_hseq>KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ</Hsp_hseq> + <Hsp_midline>KEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>3</Hsp_num> + <Hsp_bit-score>121.324</Hsp_bit-score> + <Hsp_score>303</Hsp_score> + <Hsp_evalue>1.96633e-33</Hsp_evalue> + <Hsp_query-from>2855</Hsp_query-from> + <Hsp_query-to>3031</Hsp_query-to> + <Hsp_hit-from>177</Hsp_hit-from> + <Hsp_hit-to>235</Hsp_hit-to> + <Hsp_query-frame>2</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>54</Hsp_identity> + <Hsp_positive>57</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>59</Hsp_align-len> + <Hsp_qseq>RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS</Hsp_qseq> + <Hsp_hseq>RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA</Hsp_hseq> + <Hsp_midline>RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE +</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>4</Hsp_num> + <Hsp_bit-score>97.0561</Hsp_bit-score> + <Hsp_score>240</Hsp_score> + <Hsp_evalue>1.16473e-25</Hsp_evalue> + <Hsp_query-from>1404</Hsp_query-from> + <Hsp_query-to>1580</Hsp_query-to> + <Hsp_hit-from>119</Hsp_hit-from> + <Hsp_hit-to>177</Hsp_hit-to> + <Hsp_query-frame>3</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>55</Hsp_identity> + <Hsp_positive>56</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>59</Hsp_align-len> + <Hsp_qseq>LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR</Hsp_qseq> + <Hsp_hseq>LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR</Hsp_hseq> + <Hsp_midline>L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>5</Hsp_num> + <Hsp_bit-score>56.9954</Hsp_bit-score> + <Hsp_score>136</Hsp_score> + <Hsp_evalue>1.23645e-12</Hsp_evalue> + <Hsp_query-from>4222</Hsp_query-from> + <Hsp_query-to>4299</Hsp_query-to> + <Hsp_hit-from>312</Hsp_hit-from> + <Hsp_hit-to>337</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>23</Hsp_identity> + <Hsp_positive>24</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>26</Hsp_align-len> + <Hsp_qseq>QFRNCMLTTLCCGKNPLGDDEASTTA</Hsp_qseq> + <Hsp_hseq>QFRNCMLTTICCGKNPLGDDEASATV</Hsp_hseq> + <Hsp_midline>QFRNCMLTT+CCGKNPLGDDEAS T </Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>40</Statistics_hsp-len> + <Statistics_eff-space>509838</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>13</Iteration_iter-num> + <Iteration_query-ID>Query_4</Iteration_query-ID> + <Iteration_query-def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Iteration_query-def> + <Iteration_query-len>983</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>29</Statistics_hsp-len> + <Statistics_eff-space>112346</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>14</Iteration_iter-num> + <Iteration_query-ID>Query_4</Iteration_query-ID> + <Iteration_query-def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Iteration_query-def> + <Iteration_query-len>983</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>29</Statistics_hsp-len> + <Statistics_eff-space>112346</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>15</Iteration_iter-num> + <Iteration_query-ID>Query_4</Iteration_query-ID> + <Iteration_query-def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Iteration_query-def> + <Iteration_query-len>983</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>29</Statistics_hsp-len> + <Statistics_eff-space>112346</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>16</Iteration_iter-num> + <Iteration_query-ID>Query_4</Iteration_query-ID> + <Iteration_query-def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Iteration_query-def> + <Iteration_query-len>983</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>Subject_4</Hit_id> + <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def> + <Hit_accession>Subject_4</Hit_accession> + <Hit_len>348</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>589.341</Hsp_bit-score> + <Hsp_score>1518</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>978</Hsp_query-to> + <Hsp_hit-from>11</Hsp_hit-from> + <Hsp_hit-to>336</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>310</Hsp_identity> + <Hsp_positive>322</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>326</Hsp_align-len> + <Hsp_qseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT</Hsp_qseq> + <Hsp_hseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT</Hsp_hseq> + <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>29</Statistics_hsp-len> + <Statistics_eff-space>112346</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>17</Iteration_iter-num> + <Iteration_query-ID>Query_5</Iteration_query-ID> + <Iteration_query-def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Iteration_query-def> + <Iteration_query-len>1047</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119944</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>18</Iteration_iter-num> + <Iteration_query-ID>Query_5</Iteration_query-ID> + <Iteration_query-def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Iteration_query-def> + <Iteration_query-len>1047</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119944</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>19</Iteration_iter-num> + <Iteration_query-ID>Query_5</Iteration_query-ID> + <Iteration_query-def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Iteration_query-def> + <Iteration_query-len>1047</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119944</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>20</Iteration_iter-num> + <Iteration_query-ID>Query_5</Iteration_query-ID> + <Iteration_query-def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Iteration_query-def> + <Iteration_query-len>1047</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>Subject_4</Hit_id> + <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def> + <Hit_accession>Subject_4</Hit_accession> + <Hit_len>348</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>619.387</Hsp_bit-score> + <Hsp_score>1596</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>1044</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>348</Hsp_hit-to> + <Hsp_query-frame>1</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>325</Hsp_identity> + <Hsp_positive>337</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>348</Hsp_align-len> + <Hsp_qseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_qseq> + <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_hseq> + <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>30</Statistics_hsp-len> + <Statistics_eff-space>119944</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>21</Iteration_iter-num> + <Iteration_query-ID>Query_6</Iteration_query-ID> + <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def> + <Iteration_query-len>1344</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>32</Statistics_hsp-len> + <Statistics_eff-space>155584</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>22</Iteration_iter-num> + <Iteration_query-ID>Query_6</Iteration_query-ID> + <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def> + <Iteration_query-len>1344</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>32</Statistics_hsp-len> + <Statistics_eff-space>155584</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>23</Iteration_iter-num> + <Iteration_query-ID>Query_6</Iteration_query-ID> + <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def> + <Iteration_query-len>1344</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>32</Statistics_hsp-len> + <Statistics_eff-space>155584</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>24</Iteration_iter-num> + <Iteration_query-ID>Query_6</Iteration_query-ID> + <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def> + <Iteration_query-len>1344</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>Subject_4</Hit_id> + <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def> + <Hit_accession>Subject_4</Hit_accession> + <Hit_len>348</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>532.717</Hsp_bit-score> + <Hsp_score>1371</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>23</Hsp_query-from> + <Hsp_query-to>1021</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>333</Hsp_hit-to> + <Hsp_query-frame>2</Hsp_query-frame> + <Hsp_hit-frame>0</Hsp_hit-frame> + <Hsp_identity>272</Hsp_identity> + <Hsp_positive>307</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>333</Hsp_align-len> + <Hsp_qseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG</Hsp_qseq> + <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA</Hsp_hseq> + <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +++ </Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>32</Statistics_hsp-len> + <Statistics_eff-space>155584</Statistics_eff-space> + <Statistics_kappa>0.041</Statistics_kappa> + <Statistics_lambda>0.267</Statistics_lambda> + <Statistics_entropy>0.14</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +</BlastOutput_iterations> +</BlastOutput> +
--- a/test-data/blastx_rhodopsin_vs_four_human_converted.tabular Mon Sep 23 06:14:13 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted.tabular Thu Dec 05 06:55:59 2013 -0500 @@ -1,10 +1,10 @@ -gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 662 -gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 575 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-68 224 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-36 129 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 3e-33 120 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 2e-32 118 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 2e-12 56.2 -gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 613 -gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 641 -gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 0.0 559 +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532
--- a/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Mon Sep 23 06:14:13 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Thu Dec 05 06:55:59 2013 -0500 @@ -1,10 +1,10 @@ -gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 662 sp|P08100|OPSD_HUMAN 1707 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 -gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 575 sp|P08100|OPSD_HUMAN 1481 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-68 224 sp|P08100|OPSD_HUMAN 570 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-36 129 sp|P08100|OPSD_HUMAN 324 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 3e-33 120 sp|P08100|OPSD_HUMAN 302 54 56 0 100.00 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 2e-32 118 sp|P08100|OPSD_HUMAN 295 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 2e-12 56.2 sp|P08100|OPSD_HUMAN 134 23 24 0 96.00 1 0 QFRNCMLTTLCCGKNPLGDDEASTT QFRNCMLTTICCGKNPLGDDEASAT 4301 348 -gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 613 sp|P08100|OPSD_HUMAN 1582 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 -gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 641 sp|P08100|OPSD_HUMAN 1654 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 -gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 0.0 559 sp|P08100|OPSD_HUMAN 1440 272 307 0 92.47 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1344 348 +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 sp|P08100|OPSD_HUMAN 1647 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 sp|P08100|OPSD_HUMAN 1419 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 sp|P08100|OPSD_HUMAN 560 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 sp|P08100|OPSD_HUMAN 319 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 sp|P08100|OPSD_HUMAN 303 54 57 0 96.61 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 sp|P08100|OPSD_HUMAN 240 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 sp|P08100|OPSD_HUMAN 136 23 24 0 92.31 1 0 QFRNCMLTTLCCGKNPLGDDEASTTA QFRNCMLTTICCGKNPLGDDEASATV 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 sp|P08100|OPSD_HUMAN 1518 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 sp|P08100|OPSD_HUMAN 1596 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 sp|P08100|OPSD_HUMAN 1371 272 307 0 92.19 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA 1344 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
--- a/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Mon Sep 23 06:14:13 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Thu Dec 05 06:55:59 2013 -0500 @@ -1,10 +1,10 @@ -gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 662 sp|P08100|OPSD_HUMAN 1707 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 -gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 575 sp|P08100|OPSD_HUMAN 1481 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-68 224 sp|P08100|OPSD_HUMAN 570 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-36 129 sp|P08100|OPSD_HUMAN 324 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 3e-33 120 sp|P08100|OPSD_HUMAN 302 54 56 0 100.00 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 2e-32 118 sp|P08100|OPSD_HUMAN 295 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 2e-12 56.2 sp|P08100|OPSD_HUMAN 134 23 24 0 96.00 1 0 QFRNCMLTTLCCGKNPLGDDEASTT QFRNCMLTTICCGKNPLGDDEASAT 4301 348 -gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 613 sp|P08100|OPSD_HUMAN 1582 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 -gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 641 sp|P08100|OPSD_HUMAN 1654 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 -gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 0.0 559 sp|P08100|OPSD_HUMAN 1440 272 307 0 92.47 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1344 348 +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 sp|P08100|OPSD_HUMAN 1647 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 sp|P08100|OPSD_HUMAN 1419 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 sp|P08100|OPSD_HUMAN 560 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 sp|P08100|OPSD_HUMAN 319 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 sp|P08100|OPSD_HUMAN 303 54 57 0 96.61 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 4301 348 N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 sp|P08100|OPSD_HUMAN 240 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 sp|P08100|OPSD_HUMAN 136 23 24 0 92.31 1 0 QFRNCMLTTLCCGKNPLGDDEASTTA QFRNCMLTTICCGKNPLGDDEASATV 4301 348 N/A +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 sp|P08100|OPSD_HUMAN 1518 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 N/A +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 sp|P08100|OPSD_HUMAN 1596 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 sp|P08100|OPSD_HUMAN 1371 272 307 0 92.19 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA 1344 348 N/A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dustmasker_three_human.fasta Thu Dec 05 06:55:59 2013 -0500 @@ -0,0 +1,183 @@ +>ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds +GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAG +CCCTTTCCTAACCCAACCCAACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCAC +GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC +CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA +TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC +TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT +TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA +CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA +TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA +CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC +TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA +TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT +TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG +GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA +TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA +ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG +TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA +CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC +AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT +CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA +ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC +CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA +TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG +CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC +TATGTGTatttttattttgaataaacagaaagaaattttgggtttttaatttttttCTCC +CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTaaaaaaaaaaaaaCCTGCTA +GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT +ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA +GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT +CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT +GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA +TTGCTTATGAAAATTCCATAGTGGTAtttttttGGATTCTTAATGTGTAACTTAAACATA +CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA +AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG +GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG +AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT +TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT +TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACtt +tttttCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG +CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA +CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT +TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC +TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT +GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT +AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT +TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT +GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT +TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA +GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA +TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA +TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT +AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT +TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT +ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT +GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA +GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT +GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT +TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT +TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT +AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG +AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC +TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT +CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAA +GACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT +TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCT +GAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCT +TTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGG +GCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAA +CAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCA +CGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTA +GAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGA +GGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCT +GCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATG +GAAACTTTTAGATGACATTCTACAAATTAtttttttCTTTAAATTAAAAGAACCTAGCCA +ATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCA +AAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAA +ATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAA +GGTTGTCAAGAAGGCttttttttttttcttttttAAACCTGAGGGCAAAAAGGAATGGAT +AAAGTAGTGTAATGGATTGACAATCAGGAAGAACAGAATAACTCAGtttttttttCTCCT +ACAAGGAGATATGGCTGGACCAAAATAAAATGACATGAAATTGCAAAAATGAAAAT +>ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds +GGGGGGCTGCGCGGCCGGGTCGGTGCGCACACGAGAAGGACGCGCGGCCCCCAGCGCTCT +TGGGGGCCGCCTCGGAGCATGACCCCCGCGGGCCAGCGCCGCGCGCCTGATCCGAGGAGA +CCCCGCGCTCCCGCAGCCAtgggcaccgggggccggcggggggcggcggccgcgccgctg +ctggtggcggtggccgcgctgctactgggcgccgcgggccACCTGTACCCCGGAGAGGTG +TGTCCCGGCATGGATATCCGGAACAACCTCACTAGGTTGCATGAGCTGGAGAATTGCTCT +GTCATCGAAGGACACTTGCAGATACTCTTGATGTTCAAAACGAGGCCCGAAGATTTCCGA +GACCTCAGTTTCCCCAAACTCATCATGATCACTGATTACTTGCTGCTCTTCCGGGTCTAT +GGGCTCGAGAGCCTGAAGGACCTGTTCCCCAACCTCACGGTCATCCGGGGATCACGACTG +TTCTTTAACTACGCGCTGGTCATCTTCGAGATGGTTCACCTCAAGGAACTCGGCCTCTAC +AACCTGATGAACATCACCCGGGGTTCTGTCCGCATCGAGAAGAACAATGAGCTCTGTTAC +TTGGCCACTATCGACTGGTCCCGTATCCTGGATTCCGTGGAGGATAATCACATCGTGTTG +AACAAAGATGACAACGAGGAGTGTGGAGACATCTGTCCGGGTACCGCGAAGGGCAAGACC +AACTGCCCCGCCACCGTCATCAACGGGCAGTTTGTCGAACGATGTTGGACTCATAGTCAC +TGCCAGAAAGTTTGCCCGACCATCTGTAAGTCACACGGCTGCACCGCCGAAGGCCTCTGT +TGCCACAGCGAGTGCCTGGGCAACTGTTCTCAGCCCGACGACCCCACCAAGTGCGTGGCC +TGCCGCAACTTCTACCTGGACGGCAGGTGTGTGGAGACCTGCCCGCCCCCGTACTACCAC +TTCCAGGACTGGCGCTGTGTGAACTTCAGCTTCTGCCAGGACCTGCACCACAAATGCAAG +AACTCGCGGAGGCAGGGCTGCCACCAATACGTCATTCACAACAACAAGTGCATCCCTGAG +TGTCCCTCCGGGTACACGATGAATTCCAGCAACTTGCTGTGCACCCCATGCCTGGGTCCC +TGTCCCAAGGTGTGCCACCTCCTAGAAGGCGAGAAGACCATCGACTCGGTGACGTCTGCC +CAGGAGCTCCGAGGATGCACCGTCATCAACGGGAGTCTGATCATCAACATTCGAGGAGGC +AACAATCTGGCAGCTGAGCTAGAAGCCAACCTCGGCCTCATTGAAGAAATTTCAGGGTAT +CTAAAAATCCGCCGATCCTACGCTCTGGTGTCACTTTCCTTCTTCCGGAAGTTACGTCTG +ATTCGAGGAGAGACCTTGGAAATTGGGAACTACTCCTTCTATGCCTTGGACAACCAGAAC +CTAAGGCAGCTCTGGGACTGGAGCAAACACAACCTCACCACCACTCAGGGGAAACTCTTC +TTCCACTATAACCCCAAACTCTGCTTGTCAGAAATCCACAAGATGGAAGAAGTTTCAGGA +ACCAAGGGGCGCCAGGAGAGAAACGACATTGCCCTGAAGACCAATGGGGACAAGGCATCC +TGTGAAAATGAGTTACTTAAATTTTCTTACATTCGGACATCTTTTGACAAGATCTTGCTG +AGATGGGAGCCGTACTGGCCCCCCGACTTCCGAGACCTCTTGGGGTTCATGCTGTTCTAC +AAAGAGGCCCCTTATCAGAATGTGACGGAGTTCGATGGGCAGGATGCGTGTGGTTCCAAC +AGTTGGACGGTGGTAGACATTGACCCACCCCTGAGGTCCAACGACCCCAAATCACAGAAC +CACCCAGGGTGGCTGATGCGGGGTCTCAAGCCCTGGACCCAGTATGCCATCTTTGTGAAG +ACCCTGGTCACCTTTTCGGATGAACGCCGGACCTATGGGGCCAAGAGTGACATCATTTAT +GTCCAGACAGATGCCACCAACCCCTCTGTGCCCCTGGATCCAATCTCAGTGTCTAACTCA +TCATCCCAGATTATTCTGAAGTGGAAACCACCCTCCGACCCCAATGGCAACATCACCCAC +TACCTGGTTTTCTGGGAGAGGCAGGCGGAAGACAGTGAGCTGTTCGAGCTGGATTATTGC +CTCAAAGGGCTGAAGCTGCCCTCGAGGACCTGGTCTCCACCATTCGAGTCTGAAGATTCT +CAGAAGCACAACCAGAGTGAGTATGAGGATTCGGCCGGCGAATGCTGCTCCTGTCCAAAG +ACAGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCCTCGTTTAGGAAGACGTTTGAGGAT +TACCTGCACAACGTGGTTTTCGTCCCCAGAAAAACCTCTTCAGGCACTGGTGCCGAGGAC +CCTAGGCCATCTCGGAAACGCAGGTCCCTTGGCGATGTTGGGAATGTGACGGTGGCCGTG +CCCACGGTGGCAGCTTTCCCCAACACTTCCTCGACCAGCGTGCCCACGAGTCCGGAGGAG +CACAGGCCTTTTGAGAAGGTGGTGAACAAGGAGTCGCTGGTCATCTCCGGCTTGCGACAC +TTCACGGGCTATCGCATCGAGCTGCAGGCTTGCAACCAGGACACCCCTGAGGAACGGTGC +AGTGTGGCAGCCTACGTCAGTGCGAGGACCATGCCTGAAGCCAAGGCTGATGACATTGTT +GGCCCTGTGACGCATGAAATCTTTGAGAACAACGTCGTCCACTTGATGTGGCAGGAGCCG +AAGGAGCCCAATGGTCTGATCGTGCTGTATGAAGTGAGTTATCGGCGATATGGTGATGAG +GAGCTGCATCTCTGCGTCTCCCGCAAGCACTTCGCTCTGGAACGGGGCTGCAGGCTGCGT +GGGCTGTCACCGGGGAACTACAGCGTGCGAATCCGGGCCACCTCCCTTGCGGGCAACGGC +TCTTGGACGGAACCCACCTATTTCTACGTGACAGACTATTTAGACGTCCCGTCAAATATT +GCAAAAATTATCATCGGCCCCCTCATCTTTGTCTTTCTCTTCAGTGTTGTGATTGGAAGT +ATTTATCTATTCCTGAGAAAGAGGCAGCCAGATGGGCCGCTGGGACCGCTTTACGCTTCT +TCAAACCCTGAGTATCTCAGTGCCAGTGATGTGTTTCCATGCTCTGTGTACGTGCCGGAC +GAGTGGGAGGTGTCTCGAGAGAAGATCACCCTCCTTCGAGAGCTGGGGCAGGGCTCCTTC +GGCATGGTGTATGAGGGCAATGCCAGGGACATCATCAAGGGTGAGGCAGAGACCCGCGTG +GCGGTGAAGACGGTCAACGAGTCAGCCAGTCTCCGAGAGCGGATTGAGTTCCTCAATGAG +GCCTCGGTCATGAAGGGCTTCACCTGCCATCACGTGGTGCGCCTCCTGGGAGTGGTGTCC +AAGGGCCAGCCCACGCTGGTGGTGATGGAGCTGATGGCTCACGGAGACCTGAAGAGCTAC +CTCCGTTCTCTGCGGCCAGAGGCTGAGAATAATCCTGGCCGCCCTCCCCCTACCCTTCAA +GAGATGATTCAGATGGCGGCAGAGATTGCTGACGGGATGGCCTACCTGAACGCCAAGAAG +TTTGTGCATCGGGACCTGGCAGCGAGAAACTGCATGGTCGCCCATGATTTTACTGTCAAA +ATTGGAGACTTTGGAATGACCAGAGACATCTATGAAACGGATTACTACCGGAAAGGGGGC +AAGGGTCTGCTCCCTGTACGGTGGATGGCACCGGAGTCCCTGAAGGATGGGGTCTTCACC +ACTTCTTCTGACATGTGGTCCTTTGGCGTGGTCCTTTGGGAAATCACCAGCTTGGCAGAA +CAGCCTTACCAAGGCCTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGGTAT +CTGGATCAACCCGACAACTGTCCAGAGAGAGTCACTGACCTCATGCGCATGTGCTGGCAA +TTCAACCCCAAGATGAGGCCAACCTTCCTGGAGATTGTCAACCTGCTCAAGGACGACCTG +CACCCCAGCTTTCCAGAGGTGTCGTTCTTCCACAGCGAGGAGAACAAGGCTCCCGAGAGT +GAGGAGCTGGAGATGGAGTTTGAGGACATGGAGAATGTGCCCCTGGACCGTTCCTCGCAC +TGTCAGAGGGAGGAGGCGGGGGGCCGGGATGGAGGGTCCTCGCTGGGTTTCAAGCGGAGC +TACGAGGAACACATCCCTTACACACACATGAACGGAGGCAAGAAAAACGGGCGGATTCTG +ACCTTGCCTCGGTCCAATCCTTCCTAACAGTGCCTACCGTGGCGGGGGCGGGCAGGGGTT +CCCATTTTCGCTTTCCTCTGGTTTGAAAGCCTCTGGAAAACTCAGGATTCTCACGACTCT +ACCATGTCCAGTGGAGTTCAGAGATCGTTCCTATACATTTCTGTTCATCTTAAGGTGGAC +TCGTTTGGTTACCAATTTAACTAGTCCTGCAGAGGATTTAACTGTGAACCTGGAGGGCAA +GGGGTTTCCACAGTTGCTGCTCCTTTGGGGCAACGACGGTTTCAAACCAGGATTTTGTGT +TTTTTCGTTccccccacccgcccccAGCAGATGGAAAGAAAGCACCTGTTTTTACAAATT +CttttttttttttttttttttttttttttGCTGGTGTCTGAGCTTCAGTATAAAAGACAA +AACTTCCTGTTTGTGGAACAAAATTTCGAAAGAAAAAACCAAA +>ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds +CCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAGCATTCTTGGGTGGGAGCAGC +CACGGGTCAGCCACAAGGGCCACAGCCATGAATGGCACAGAAGGCCCTAACTTCTACGTG +CCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTG +GCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGC +TTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCT +CTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTC +ACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAAT +TTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTG +GCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAAC +CATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCA +CTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTAC +TACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCAC +TTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAG +GAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACC +CGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTG +GCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCA +GCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAG +CAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGAT +GAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAAGACCTG +CCTAGGACTCTGTGGCCGACTATAGGCGTCTCCCATCCCCTACACCTTCCCCCAGCCACA +GCCATCCCACCAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dustmasker_three_human.maskinfo-asn1 Thu Dec 05 06:55:59 2013 -0500 @@ -0,0 +1,64 @@ +Blast-db-mask-info ::= { + algo-id 2, + algo-program dust, + algo-options "window=64; level=20; linker=1", + masks { + masks { + packed-int { + { + from 1447, + to 1495, + id local id 1 + }, + { + from 1540, + to 1552, + id local id 1 + }, + { + from 1886, + to 1892, + id local id 1 + }, + { + from 2278, + to 2284, + id local id 1 + }, + { + from 4409, + to 4415, + id local id 1 + }, + { + from 4635, + to 4653, + id local id 1 + }, + { + from 4726, + to 4734, + id local id 1 + } + }, + packed-int { + { + from 139, + to 219, + id local id 2 + }, + { + from 4569, + to 4584, + id local id 2 + }, + { + from 4621, + to 4648, + id local id 2 + } + } + }, + more FALSE + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.fasta.log Thu Dec 05 06:55:59 2013 -0500 @@ -0,0 +1,10 @@ + + +Building a new DB, current time: 11/21/2013 11:16:27 +New DB name: /tmp/tmpnSjpCP/tmpwAbNo4/database/files/000/dataset_2_files/blastdb +New DB title: Just 4 human proteins +Sequence type: Protein +Keep Linkouts: T +Keep MBits: T +Maximum file size: 1000000000B +Adding sequences from FASTA; added 4 sequences in 0.00202417 seconds.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.fasta.phd Thu Dec 05 06:55:59 2013 -0500 @@ -0,0 +1,4 @@ +11117184492 +29249033410 +36665887501 +5392473183
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.fasta.psd Thu Dec 05 06:55:59 2013 -0500 @@ -0,0 +1,4 @@ +gnl|bl_ord_id|00 +gnl|bl_ord_id|11 +gnl|bl_ord_id|22 +gnl|bl_ord_id|33
--- a/test-data/tblastn_four_human_vs_rhodopsin.html Mon Sep 23 06:14:13 2013 -0400 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Thu Dec 05 06:55:59 2013 -0500 @@ -3,7 +3,7 @@ <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099"> <PRE> -<b>TBLASTN 2.2.26+</b> +<b>TBLASTN 2.2.28+</b> <b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 @@ -20,12 +20,12 @@ -Lambda K H - 0.347 0.182 0.684 +Lambda K H a alpha + 0.347 0.182 0.684 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 127710 @@ -45,12 +45,12 @@ -Lambda K H - 0.347 0.182 0.684 +Lambda K H a alpha + 0.347 0.182 0.684 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 127710 @@ -70,12 +70,12 @@ -Lambda K H - 0.347 0.182 0.684 +Lambda K H a alpha + 0.347 0.182 0.684 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 127710 @@ -95,12 +95,12 @@ -Lambda K H - 0.347 0.182 0.684 +Lambda K H a alpha + 0.347 0.182 0.684 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 127710 @@ -120,12 +120,12 @@ -Lambda K H - 0.347 0.182 0.684 +Lambda K H a alpha + 0.347 0.182 0.684 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 127710 @@ -145,12 +145,12 @@ -Lambda K H - 0.347 0.182 0.684 +Lambda K H a alpha + 0.347 0.182 0.684 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 127710 @@ -169,12 +169,12 @@ -Lambda K H - 0.334 0.170 0.615 +Lambda K H a alpha + 0.334 0.170 0.615 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 370988 @@ -194,12 +194,12 @@ -Lambda K H - 0.334 0.170 0.615 +Lambda K H a alpha + 0.334 0.170 0.615 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 370988 @@ -219,12 +219,12 @@ -Lambda K H - 0.334 0.170 0.615 +Lambda K H a alpha + 0.334 0.170 0.615 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 370988 @@ -244,12 +244,12 @@ -Lambda K H - 0.334 0.170 0.615 +Lambda K H a alpha + 0.334 0.170 0.615 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 370988 @@ -269,12 +269,12 @@ -Lambda K H - 0.334 0.170 0.615 +Lambda K H a alpha + 0.334 0.170 0.615 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 370988 @@ -294,12 +294,12 @@ -Lambda K H - 0.334 0.170 0.615 +Lambda K H a alpha + 0.334 0.170 0.615 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 370988 @@ -318,12 +318,12 @@ -Lambda K H - 0.346 0.180 0.700 +Lambda K H a alpha + 0.346 0.180 0.700 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 441350 @@ -343,12 +343,12 @@ -Lambda K H - 0.346 0.180 0.700 +Lambda K H a alpha + 0.346 0.180 0.700 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 441350 @@ -368,12 +368,12 @@ -Lambda K H - 0.346 0.180 0.700 +Lambda K H a alpha + 0.346 0.180 0.700 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 441350 @@ -393,12 +393,12 @@ -Lambda K H - 0.346 0.180 0.700 +Lambda K H a alpha + 0.346 0.180 0.700 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 441350 @@ -418,12 +418,12 @@ -Lambda K H - 0.346 0.180 0.700 +Lambda K H a alpha + 0.346 0.180 0.700 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 441350 @@ -443,12 +443,12 @@ -Lambda K H - 0.346 0.180 0.700 +Lambda K H a alpha + 0.346 0.180 0.700 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 441350 @@ -492,12 +492,12 @@ -Lambda K H - 0.351 0.182 0.707 +Lambda K H a alpha + 0.351 0.182 0.707 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 109230 @@ -542,12 +542,12 @@ -Lambda K H - 0.351 0.182 0.707 +Lambda K H a alpha + 0.351 0.182 0.707 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 109230 @@ -616,12 +616,12 @@ -Lambda K H - 0.351 0.182 0.707 +Lambda K H a alpha + 0.351 0.182 0.707 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 109230 @@ -666,12 +666,12 @@ -Lambda K H - 0.351 0.182 0.707 +Lambda K H a alpha + 0.351 0.182 0.707 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 109230 @@ -716,12 +716,12 @@ -Lambda K H - 0.351 0.182 0.707 +Lambda K H a alpha + 0.351 0.182 0.707 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 109230 @@ -766,12 +766,12 @@ -Lambda K H - 0.351 0.182 0.707 +Lambda K H a alpha + 0.351 0.182 0.707 0.522 1.92 Gapped -Lambda K H - 0.299 0.0710 0.270 +Lambda K H a alpha sigma + 0.299 0.0710 0.270 1.10 13.8 14.5 Effective search space used: 109230
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/test-data/tblastn_four_human_vs_rhodopsin.xml Thu Dec 05 06:55:59 2013 -0500 @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>tblastn</BlastOutput_program> - <BlastOutput_version>TBLASTN 2.2.26+</BlastOutput_version> + <BlastOutput_version>TBLASTN 2.2.28+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> @@ -17,706 +17,725 @@ <Parameters_filter>F</Parameters_filter> </Parameters> </BlastOutput_param> - <BlastOutput_iterations> - <Iteration> - <Iteration_iter-num>1</Iteration_iter-num> - <Iteration_query-ID>Query_1</Iteration_query-ID> - <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>406</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>19</Statistics_hsp-len> - <Statistics_eff-space>127710</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>2</Iteration_iter-num> - <Iteration_query-ID>Query_1</Iteration_query-ID> - <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>406</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>19</Statistics_hsp-len> - <Statistics_eff-space>127710</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>3</Iteration_iter-num> - <Iteration_query-ID>Query_1</Iteration_query-ID> - <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>406</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>19</Statistics_hsp-len> - <Statistics_eff-space>127710</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>4</Iteration_iter-num> - <Iteration_query-ID>Query_1</Iteration_query-ID> - <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>406</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>19</Statistics_hsp-len> - <Statistics_eff-space>127710</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>5</Iteration_iter-num> - <Iteration_query-ID>Query_1</Iteration_query-ID> - <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>406</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>19</Statistics_hsp-len> - <Statistics_eff-space>127710</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>6</Iteration_iter-num> - <Iteration_query-ID>Query_1</Iteration_query-ID> - <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>406</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>19</Statistics_hsp-len> - <Statistics_eff-space>127710</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>7</Iteration_iter-num> - <Iteration_query-ID>Query_2</Iteration_query-ID> - <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> - <Iteration_query-len>1161</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>23</Statistics_hsp-len> - <Statistics_eff-space>370988</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>8</Iteration_iter-num> - <Iteration_query-ID>Query_2</Iteration_query-ID> - <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> - <Iteration_query-len>1161</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>23</Statistics_hsp-len> - <Statistics_eff-space>370988</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>9</Iteration_iter-num> - <Iteration_query-ID>Query_2</Iteration_query-ID> - <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> - <Iteration_query-len>1161</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>23</Statistics_hsp-len> - <Statistics_eff-space>370988</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>10</Iteration_iter-num> - <Iteration_query-ID>Query_2</Iteration_query-ID> - <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> - <Iteration_query-len>1161</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>23</Statistics_hsp-len> - <Statistics_eff-space>370988</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>11</Iteration_iter-num> - <Iteration_query-ID>Query_2</Iteration_query-ID> - <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> - <Iteration_query-len>1161</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>23</Statistics_hsp-len> - <Statistics_eff-space>370988</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>12</Iteration_iter-num> - <Iteration_query-ID>Query_2</Iteration_query-ID> - <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> - <Iteration_query-len>1161</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>23</Statistics_hsp-len> - <Statistics_eff-space>370988</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>13</Iteration_iter-num> - <Iteration_query-ID>Query_3</Iteration_query-ID> - <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> - <Iteration_query-len>1382</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>24</Statistics_hsp-len> - <Statistics_eff-space>441350</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>14</Iteration_iter-num> - <Iteration_query-ID>Query_3</Iteration_query-ID> - <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> - <Iteration_query-len>1382</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>24</Statistics_hsp-len> - <Statistics_eff-space>441350</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>15</Iteration_iter-num> - <Iteration_query-ID>Query_3</Iteration_query-ID> - <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> - <Iteration_query-len>1382</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>24</Statistics_hsp-len> - <Statistics_eff-space>441350</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>16</Iteration_iter-num> - <Iteration_query-ID>Query_3</Iteration_query-ID> - <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> - <Iteration_query-len>1382</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>24</Statistics_hsp-len> - <Statistics_eff-space>441350</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>17</Iteration_iter-num> - <Iteration_query-ID>Query_3</Iteration_query-ID> - <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> - <Iteration_query-len>1382</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>24</Statistics_hsp-len> - <Statistics_eff-space>441350</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>18</Iteration_iter-num> - <Iteration_query-ID>Query_3</Iteration_query-ID> - <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> - <Iteration_query-len>1382</Iteration_query-len> - <Iteration_hits></Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>24</Statistics_hsp-len> - <Statistics_eff-space>441350</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - <Iteration_message>No hits found</Iteration_message> - </Iteration> - <Iteration> - <Iteration_iter-num>19</Iteration_iter-num> - <Iteration_query-ID>Query_4</Iteration_query-ID> - <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>348</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>Subject_1</Hit_id> - <Hit_def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Hit_def> - <Hit_accession>Subject_1</Hit_accession> - <Hit_len>1047</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>732.393</Hsp_bit-score> - <Hsp_score>1689</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>1</Hsp_query-from> - <Hsp_query-to>348</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>1044</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>1</Hsp_hit-frame> - <Hsp_identity>336</Hsp_identity> - <Hsp_positive>343</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>348</Hsp_align-len> - <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq> - <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA</Hsp_hseq> - <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>18</Statistics_hsp-len> - <Statistics_eff-space>109230</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>20</Iteration_iter-num> - <Iteration_query-ID>Query_4</Iteration_query-ID> - <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>348</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>Subject_2</Hit_id> - <Hit_def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Hit_def> - <Hit_accession>Subject_2</Hit_accession> - <Hit_len>1574</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>646.12</Hsp_bit-score> - <Hsp_score>1489</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>1</Hsp_query-from> - <Hsp_query-to>341</Hsp_query-to> - <Hsp_hit-from>42</Hsp_hit-from> - <Hsp_hit-to>1067</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>3</Hsp_hit-frame> - <Hsp_identity>290</Hsp_identity> - <Hsp_positive>320</Hsp_positive> - <Hsp_gaps>1</Hsp_gaps> - <Hsp_align-len>342</Hsp_align-len> - <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE</Hsp_qseq> - <Hsp_hseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE</Hsp_hseq> - <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S+ GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF+ QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA SKTE</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>18</Statistics_hsp-len> - <Statistics_eff-space>109230</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>21</Iteration_iter-num> - <Iteration_query-ID>Query_4</Iteration_query-ID> - <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>348</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>Subject_3</Hit_id> - <Hit_def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Hit_def> - <Hit_accession>Subject_3</Hit_accession> - <Hit_len>4301</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>151.343</Hsp_bit-score> - <Hsp_score>342</Hsp_score> - <Hsp_evalue>1.39567e-72</Hsp_evalue> - <Hsp_query-from>239</Hsp_query-from> - <Hsp_query-to>312</Hsp_query-to> - <Hsp_hit-from>3147</Hsp_hit-from> - <Hsp_hit-to>3368</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>3</Hsp_hit-frame> - <Hsp_identity>69</Hsp_identity> - <Hsp_positive>73</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>74</Hsp_align-len> - <Hsp_qseq>ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ</Hsp_qseq> - <Hsp_hseq>ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ</Hsp_hseq> - <Hsp_midline>ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ</Hsp_midline> - </Hsp> - <Hsp> - <Hsp_num>2</Hsp_num> - <Hsp_bit-score>126.324</Hsp_bit-score> - <Hsp_score>284</Hsp_score> - <Hsp_evalue>1.39567e-72</Hsp_evalue> - <Hsp_query-from>177</Hsp_query-from> - <Hsp_query-to>235</Hsp_query-to> - <Hsp_hit-from>2855</Hsp_hit-from> - <Hsp_hit-to>3031</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>2</Hsp_hit-frame> - <Hsp_identity>54</Hsp_identity> - <Hsp_positive>57</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>59</Hsp_align-len> - <Hsp_qseq>RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA</Hsp_qseq> - <Hsp_hseq>RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS</Hsp_hseq> - <Hsp_midline>RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE +</Hsp_midline> - </Hsp> - <Hsp> - <Hsp_num>3</Hsp_num> - <Hsp_bit-score>229.42</Hsp_bit-score> - <Hsp_score>523</Hsp_score> - <Hsp_evalue>9.34154e-67</Hsp_evalue> - <Hsp_query-from>11</Hsp_query-from> - <Hsp_query-to>121</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>333</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>1</Hsp_hit-frame> - <Hsp_identity>107</Hsp_identity> - <Hsp_positive>109</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>111</Hsp_align-len> - <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_qseq> - <Hsp_hseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_hseq> - <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_midline> - </Hsp> - <Hsp> - <Hsp_num>4</Hsp_num> - <Hsp_bit-score>122.873</Hsp_bit-score> - <Hsp_score>276</Hsp_score> - <Hsp_evalue>1.03783e-32</Hsp_evalue> - <Hsp_query-from>119</Hsp_query-from> - <Hsp_query-to>177</Hsp_query-to> - <Hsp_hit-from>1404</Hsp_hit-from> - <Hsp_hit-to>1580</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>3</Hsp_hit-frame> - <Hsp_identity>55</Hsp_identity> - <Hsp_positive>56</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>59</Hsp_align-len> - <Hsp_qseq>LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR</Hsp_qseq> - <Hsp_hseq>LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR</Hsp_hseq> - <Hsp_midline>L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR</Hsp_midline> - </Hsp> - <Hsp> - <Hsp_num>5</Hsp_num> - <Hsp_bit-score>57.7368</Hsp_bit-score> - <Hsp_score>125</Hsp_score> - <Hsp_evalue>1.50808e-12</Hsp_evalue> - <Hsp_query-from>312</Hsp_query-from> - <Hsp_query-to>337</Hsp_query-to> - <Hsp_hit-from>4222</Hsp_hit-from> - <Hsp_hit-to>4299</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>1</Hsp_hit-frame> - <Hsp_identity>23</Hsp_identity> - <Hsp_positive>24</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>26</Hsp_align-len> - <Hsp_qseq>QFRNCMLTTICCGKNPLGDDEASATV</Hsp_qseq> - <Hsp_hseq>QFRNCMLTTLCCGKNPLGDDEASTTA</Hsp_hseq> - <Hsp_midline>QFRNCMLTT+CCGKNPLGDDEAS T </Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>18</Statistics_hsp-len> - <Statistics_eff-space>109230</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>22</Iteration_iter-num> - <Iteration_query-ID>Query_4</Iteration_query-ID> - <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>348</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>Subject_4</Hit_id> - <Hit_def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Hit_def> - <Hit_accession>Subject_4</Hit_accession> - <Hit_len>983</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>658.198</Hsp_bit-score> - <Hsp_score>1517</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>11</Hsp_query-from> - <Hsp_query-to>336</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>978</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>1</Hsp_hit-frame> - <Hsp_identity>310</Hsp_identity> - <Hsp_positive>322</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>326</Hsp_align-len> - <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT</Hsp_qseq> - <Hsp_hseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT</Hsp_hseq> - <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>18</Statistics_hsp-len> - <Statistics_eff-space>109230</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>23</Iteration_iter-num> - <Iteration_query-ID>Query_4</Iteration_query-ID> - <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>348</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>Subject_5</Hit_id> - <Hit_def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Hit_def> - <Hit_accession>Subject_5</Hit_accession> - <Hit_len>1047</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>711.256</Hsp_bit-score> - <Hsp_score>1640</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>1</Hsp_query-from> - <Hsp_query-to>348</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>1044</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>1</Hsp_hit-frame> - <Hsp_identity>325</Hsp_identity> - <Hsp_positive>337</Hsp_positive> - <Hsp_gaps>0</Hsp_gaps> - <Hsp_align-len>348</Hsp_align-len> - <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq> - <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq> - <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>18</Statistics_hsp-len> - <Statistics_eff-space>109230</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - <Iteration> - <Iteration_iter-num>24</Iteration_iter-num> - <Iteration_query-ID>Query_4</Iteration_query-ID> - <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> - <Iteration_query-len>348</Iteration_query-len> - <Iteration_hits> - <Hit> - <Hit_num>1</Hit_num> - <Hit_id>Subject_6</Hit_id> - <Hit_def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Hit_def> - <Hit_accession>Subject_6</Hit_accession> - <Hit_len>1344</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>626.708</Hsp_bit-score> - <Hsp_score>1444</Hsp_score> - <Hsp_evalue>0</Hsp_evalue> - <Hsp_query-from>1</Hsp_query-from> - <Hsp_query-to>341</Hsp_query-to> - <Hsp_hit-from>23</Hsp_hit-from> - <Hsp_hit-to>1048</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>2</Hsp_hit-frame> - <Hsp_identity>281</Hsp_identity> - <Hsp_positive>311</Hsp_positive> - <Hsp_gaps>1</Hsp_gaps> - <Hsp_align-len>342</Hsp_align-len> - <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq> - <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq> - <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR CM+TT+CCGKNP +D ASAT SKTE</Hsp_midline> - </Hsp> - </Hit_hsps> - </Hit> - </Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>0</Statistics_db-num> - <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>18</Statistics_hsp-len> - <Statistics_eff-space>109230</Statistics_eff-space> - <Statistics_kappa>0.071</Statistics_kappa> - <Statistics_lambda>0.299</Statistics_lambda> - <Statistics_entropy>0.27</Statistics_entropy> - </Statistics> - </Iteration_stat> - </Iteration> - </BlastOutput_iterations> -</BlastOutput> \ No newline at end of file +<BlastOutput_iterations> +<Iteration> + <Iteration_iter-num>1</Iteration_iter-num> + <Iteration_query-ID>Query_1</Iteration_query-ID> + <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>406</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>19</Statistics_hsp-len> + <Statistics_eff-space>127710</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>2</Iteration_iter-num> + <Iteration_query-ID>Query_1</Iteration_query-ID> + <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>406</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>19</Statistics_hsp-len> + <Statistics_eff-space>127710</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>3</Iteration_iter-num> + <Iteration_query-ID>Query_1</Iteration_query-ID> + <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>406</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>19</Statistics_hsp-len> + <Statistics_eff-space>127710</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>4</Iteration_iter-num> + <Iteration_query-ID>Query_1</Iteration_query-ID> + <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>406</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>19</Statistics_hsp-len> + <Statistics_eff-space>127710</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>5</Iteration_iter-num> + <Iteration_query-ID>Query_1</Iteration_query-ID> + <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>406</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>19</Statistics_hsp-len> + <Statistics_eff-space>127710</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>6</Iteration_iter-num> + <Iteration_query-ID>Query_1</Iteration_query-ID> + <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>406</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>19</Statistics_hsp-len> + <Statistics_eff-space>127710</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>7</Iteration_iter-num> + <Iteration_query-ID>Query_2</Iteration_query-ID> + <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> + <Iteration_query-len>1161</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>23</Statistics_hsp-len> + <Statistics_eff-space>370988</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>8</Iteration_iter-num> + <Iteration_query-ID>Query_2</Iteration_query-ID> + <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> + <Iteration_query-len>1161</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>23</Statistics_hsp-len> + <Statistics_eff-space>370988</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>9</Iteration_iter-num> + <Iteration_query-ID>Query_2</Iteration_query-ID> + <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> + <Iteration_query-len>1161</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>23</Statistics_hsp-len> + <Statistics_eff-space>370988</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>10</Iteration_iter-num> + <Iteration_query-ID>Query_2</Iteration_query-ID> + <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> + <Iteration_query-len>1161</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>23</Statistics_hsp-len> + <Statistics_eff-space>370988</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>11</Iteration_iter-num> + <Iteration_query-ID>Query_2</Iteration_query-ID> + <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> + <Iteration_query-len>1161</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>23</Statistics_hsp-len> + <Statistics_eff-space>370988</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>12</Iteration_iter-num> + <Iteration_query-ID>Query_2</Iteration_query-ID> + <Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def> + <Iteration_query-len>1161</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>23</Statistics_hsp-len> + <Statistics_eff-space>370988</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>13</Iteration_iter-num> + <Iteration_query-ID>Query_3</Iteration_query-ID> + <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> + <Iteration_query-len>1382</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>24</Statistics_hsp-len> + <Statistics_eff-space>441350</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>14</Iteration_iter-num> + <Iteration_query-ID>Query_3</Iteration_query-ID> + <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> + <Iteration_query-len>1382</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>24</Statistics_hsp-len> + <Statistics_eff-space>441350</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>15</Iteration_iter-num> + <Iteration_query-ID>Query_3</Iteration_query-ID> + <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> + <Iteration_query-len>1382</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>24</Statistics_hsp-len> + <Statistics_eff-space>441350</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>16</Iteration_iter-num> + <Iteration_query-ID>Query_3</Iteration_query-ID> + <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> + <Iteration_query-len>1382</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>24</Statistics_hsp-len> + <Statistics_eff-space>441350</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>17</Iteration_iter-num> + <Iteration_query-ID>Query_3</Iteration_query-ID> + <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> + <Iteration_query-len>1382</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>24</Statistics_hsp-len> + <Statistics_eff-space>441350</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>18</Iteration_iter-num> + <Iteration_query-ID>Query_3</Iteration_query-ID> + <Iteration_query-def>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def> + <Iteration_query-len>1382</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>24</Statistics_hsp-len> + <Statistics_eff-space>441350</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +<Iteration> + <Iteration_iter-num>19</Iteration_iter-num> + <Iteration_query-ID>Query_4</Iteration_query-ID> + <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>348</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>Subject_1</Hit_id> + <Hit_def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Hit_def> + <Hit_accession>Subject_1</Hit_accession> + <Hit_len>1047</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>732.393</Hsp_bit-score> + <Hsp_score>1689</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>348</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>1044</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>336</Hsp_identity> + <Hsp_positive>343</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>348</Hsp_align-len> + <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq> + <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA</Hsp_hseq> + <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>18</Statistics_hsp-len> + <Statistics_eff-space>109230</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>20</Iteration_iter-num> + <Iteration_query-ID>Query_4</Iteration_query-ID> + <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>348</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>Subject_2</Hit_id> + <Hit_def>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds</Hit_def> + <Hit_accession>Subject_2</Hit_accession> + <Hit_len>1574</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>646.12</Hsp_bit-score> + <Hsp_score>1489</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>341</Hsp_query-to> + <Hsp_hit-from>42</Hsp_hit-from> + <Hsp_hit-to>1067</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>3</Hsp_hit-frame> + <Hsp_identity>290</Hsp_identity> + <Hsp_positive>320</Hsp_positive> + <Hsp_gaps>1</Hsp_gaps> + <Hsp_align-len>342</Hsp_align-len> + <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE</Hsp_qseq> + <Hsp_hseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE</Hsp_hseq> + <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S+ GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF+ QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA SKTE</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>18</Statistics_hsp-len> + <Statistics_eff-space>109230</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>21</Iteration_iter-num> + <Iteration_query-ID>Query_4</Iteration_query-ID> + <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>348</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>Subject_3</Hit_id> + <Hit_def>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds</Hit_def> + <Hit_accession>Subject_3</Hit_accession> + <Hit_len>4301</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>151.343</Hsp_bit-score> + <Hsp_score>342</Hsp_score> + <Hsp_evalue>1.39567e-72</Hsp_evalue> + <Hsp_query-from>239</Hsp_query-from> + <Hsp_query-to>312</Hsp_query-to> + <Hsp_hit-from>3147</Hsp_hit-from> + <Hsp_hit-to>3368</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>3</Hsp_hit-frame> + <Hsp_identity>69</Hsp_identity> + <Hsp_positive>73</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>74</Hsp_align-len> + <Hsp_qseq>ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ</Hsp_qseq> + <Hsp_hseq>ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ</Hsp_hseq> + <Hsp_midline>ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>2</Hsp_num> + <Hsp_bit-score>126.324</Hsp_bit-score> + <Hsp_score>284</Hsp_score> + <Hsp_evalue>1.39567e-72</Hsp_evalue> + <Hsp_query-from>177</Hsp_query-from> + <Hsp_query-to>235</Hsp_query-to> + <Hsp_hit-from>2855</Hsp_hit-from> + <Hsp_hit-to>3031</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>2</Hsp_hit-frame> + <Hsp_identity>54</Hsp_identity> + <Hsp_positive>57</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>59</Hsp_align-len> + <Hsp_qseq>RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA</Hsp_qseq> + <Hsp_hseq>RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS</Hsp_hseq> + <Hsp_midline>RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE +</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>3</Hsp_num> + <Hsp_bit-score>229.42</Hsp_bit-score> + <Hsp_score>523</Hsp_score> + <Hsp_evalue>9.34154e-67</Hsp_evalue> + <Hsp_query-from>11</Hsp_query-from> + <Hsp_query-to>121</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>333</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>107</Hsp_identity> + <Hsp_positive>109</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>111</Hsp_align-len> + <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_qseq> + <Hsp_hseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_hseq> + <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>4</Hsp_num> + <Hsp_bit-score>122.873</Hsp_bit-score> + <Hsp_score>276</Hsp_score> + <Hsp_evalue>1.03783e-32</Hsp_evalue> + <Hsp_query-from>119</Hsp_query-from> + <Hsp_query-to>177</Hsp_query-to> + <Hsp_hit-from>1404</Hsp_hit-from> + <Hsp_hit-to>1580</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>3</Hsp_hit-frame> + <Hsp_identity>55</Hsp_identity> + <Hsp_positive>56</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>59</Hsp_align-len> + <Hsp_qseq>LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR</Hsp_qseq> + <Hsp_hseq>LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR</Hsp_hseq> + <Hsp_midline>L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR</Hsp_midline> + </Hsp> + <Hsp> + <Hsp_num>5</Hsp_num> + <Hsp_bit-score>57.7368</Hsp_bit-score> + <Hsp_score>125</Hsp_score> + <Hsp_evalue>1.50808e-12</Hsp_evalue> + <Hsp_query-from>312</Hsp_query-from> + <Hsp_query-to>337</Hsp_query-to> + <Hsp_hit-from>4222</Hsp_hit-from> + <Hsp_hit-to>4299</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>23</Hsp_identity> + <Hsp_positive>24</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>26</Hsp_align-len> + <Hsp_qseq>QFRNCMLTTICCGKNPLGDDEASATV</Hsp_qseq> + <Hsp_hseq>QFRNCMLTTLCCGKNPLGDDEASTTA</Hsp_hseq> + <Hsp_midline>QFRNCMLTT+CCGKNPLGDDEAS T </Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>18</Statistics_hsp-len> + <Statistics_eff-space>109230</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>22</Iteration_iter-num> + <Iteration_query-ID>Query_4</Iteration_query-ID> + <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>348</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>Subject_4</Hit_id> + <Hit_def>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds</Hit_def> + <Hit_accession>Subject_4</Hit_accession> + <Hit_len>983</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>658.198</Hsp_bit-score> + <Hsp_score>1517</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>11</Hsp_query-from> + <Hsp_query-to>336</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>978</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>310</Hsp_identity> + <Hsp_positive>322</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>326</Hsp_align-len> + <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT</Hsp_qseq> + <Hsp_hseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT</Hsp_hseq> + <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>18</Statistics_hsp-len> + <Statistics_eff-space>109230</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>23</Iteration_iter-num> + <Iteration_query-ID>Query_4</Iteration_query-ID> + <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>348</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>Subject_5</Hit_id> + <Hit_def>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds</Hit_def> + <Hit_accession>Subject_5</Hit_accession> + <Hit_len>1047</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>711.256</Hsp_bit-score> + <Hsp_score>1640</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>348</Hsp_query-to> + <Hsp_hit-from>1</Hsp_hit-from> + <Hsp_hit-to>1044</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>1</Hsp_hit-frame> + <Hsp_identity>325</Hsp_identity> + <Hsp_positive>337</Hsp_positive> + <Hsp_gaps>0</Hsp_gaps> + <Hsp_align-len>348</Hsp_align-len> + <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq> + <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq> + <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>18</Statistics_hsp-len> + <Statistics_eff-space>109230</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +<Iteration> + <Iteration_iter-num>24</Iteration_iter-num> + <Iteration_query-ID>Query_4</Iteration_query-ID> + <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def> + <Iteration_query-len>348</Iteration_query-len> +<Iteration_hits> +<Hit> + <Hit_num>1</Hit_num> + <Hit_id>Subject_6</Hit_id> + <Hit_def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Hit_def> + <Hit_accession>Subject_6</Hit_accession> + <Hit_len>1344</Hit_len> + <Hit_hsps> + <Hsp> + <Hsp_num>1</Hsp_num> + <Hsp_bit-score>626.708</Hsp_bit-score> + <Hsp_score>1444</Hsp_score> + <Hsp_evalue>0</Hsp_evalue> + <Hsp_query-from>1</Hsp_query-from> + <Hsp_query-to>341</Hsp_query-to> + <Hsp_hit-from>23</Hsp_hit-from> + <Hsp_hit-to>1048</Hsp_hit-to> + <Hsp_query-frame>0</Hsp_query-frame> + <Hsp_hit-frame>2</Hsp_hit-frame> + <Hsp_identity>281</Hsp_identity> + <Hsp_positive>311</Hsp_positive> + <Hsp_gaps>1</Hsp_gaps> + <Hsp_align-len>342</Hsp_align-len> + <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq> + <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq> + <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR CM+TT+CCGKNP +D ASAT SKTE</Hsp_midline> + </Hsp> + </Hit_hsps> +</Hit> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>18</Statistics_hsp-len> + <Statistics_eff-space>109230</Statistics_eff-space> + <Statistics_kappa>0.071</Statistics_kappa> + <Statistics_lambda>0.299</Statistics_lambda> + <Statistics_entropy>0.27</Statistics_entropy> + </Statistics> + </Iteration_stat> +</Iteration> +</BlastOutput_iterations> +</BlastOutput> +
--- a/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Mon Sep 23 06:14:13 2013 -0400 +++ b/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Thu Dec 05 06:55:59 2013 -0500 @@ -1,10 +1,10 @@ -sp|P08100|OPSD_HUMAN gi|57163782|ref|NM_001009242.1| 96.55 348 12 0 1 348 1 1044 0.0 732 gi|57163782|ref|NM_001009242.1| 1689 336 343 0 98.56 0 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 1047 -sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0 646 gi|2734705|gb|U59921.1|BBU59921 1489 290 320 1 93.57 0 3 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 1574 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72 151 gi|283855845|gb|GQ290303.1| 342 69 73 0 98.65 0 3 ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ 348 4301 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72 126 gi|283855845|gb|GQ290303.1| 284 54 57 0 96.61 0 2 RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS 348 4301 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 9e-67 229 gi|283855845|gb|GQ290303.1| 523 107 109 0 98.20 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG 348 4301 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32 122 gi|283855845|gb|GQ290303.1| 276 55 56 0 94.92 0 3 LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR 348 4301 -sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 2e-12 57.7 gi|283855845|gb|GQ290303.1| 125 23 24 0 92.31 0 1 QFRNCMLTTICCGKNPLGDDEASATV QFRNCMLTTLCCGKNPLGDDEASTTA 348 4301 -sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0 658 gi|283855822|gb|GQ290312.1| 1517 310 322 0 98.77 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT 348 983 -sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0 711 gi|18148870|dbj|AB062417.1| 1640 325 337 0 96.84 0 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 1047 -sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0 626 gi|12583664|dbj|AB043817.1| 1444 281 311 1 90.94 0 2 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 1344 +sp|P08100|OPSD_HUMAN gi|57163782|ref|NM_001009242.1| 96.55 348 12 0 1 348 1 1044 0.0 732 gi|57163782|ref|NM_001009242.1| 1689 336 343 0 98.56 0 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 1047 N/A +sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0 646 gi|2734705|gb|U59921.1|BBU59921 1489 290 320 1 93.57 0 3 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 1574 N/A +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72 151 gi|283855845|gb|GQ290303.1| 342 69 73 0 98.65 0 3 ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ 348 4301 N/A +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72 126 gi|283855845|gb|GQ290303.1| 284 54 57 0 96.61 0 2 RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS 348 4301 N/A +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 9e-67 229 gi|283855845|gb|GQ290303.1| 523 107 109 0 98.20 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG 348 4301 N/A +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32 122 gi|283855845|gb|GQ290303.1| 276 55 56 0 94.92 0 3 LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR 348 4301 N/A +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 2e-12 57.7 gi|283855845|gb|GQ290303.1| 125 23 24 0 92.31 0 1 QFRNCMLTTICCGKNPLGDDEASATV QFRNCMLTTLCCGKNPLGDDEASTTA 348 4301 N/A +sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0 658 gi|283855822|gb|GQ290312.1| 1517 310 322 0 98.77 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT 348 983 N/A +sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0 711 gi|18148870|dbj|AB062417.1| 1640 325 337 0 96.84 0 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 1047 N/A +sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0 626 gi|12583664|dbj|AB043817.1| 1444 281 311 1 90.94 0 2 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 1344 N/A
--- a/tools/ncbi_blast_plus/README.rst Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/README.rst Thu Dec 05 06:55:59 2013 -0500 @@ -5,12 +5,12 @@ (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. -Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 of BLAST+), -and does not work with the NCBI 'legacy' BLAST suite (e.g. blastall). +Currently tested with NCBI BLAST 2.2.28+ (i.e. version 2.2.28 of BLAST+), +and does not work with the NCBI 'legacy' BLAST suite (e.g. ``blastall``). Note that these wrappers (and the associated datatypes) were originally distributed as part of the main Galaxy repository, but as of August 2012 -moved to the Galaxy Tool Shed as 'ncbi_blast_plus' (and 'blast_datatypes'). +moved to the Galaxy Tool Shed as ``ncbi_blast_plus`` (and ``blast_datatypes``). My thanks to Dannon Baker from the Galaxy development team for his assistance with this. @@ -22,9 +22,9 @@ ====================== Galaxy should be able to automatically install the dependencies, i.e. the -'blast_datatypes' repository which defines the BLAST XML file format -('blastxml') and protein and nucleotide BLAST databases ('blastdbp' and -'blastdbn'). +``blast_datatypes`` repository which defines the BLAST XML file format +(``blastxml``) and protein and nucleotide BLAST databases (``blastdbp`` and +``blastdbn``). You must tell Galaxy about any system level BLAST databases using configuration files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein @@ -42,9 +42,9 @@ =================== For those not using Galaxy's automated installation from the Tool Shed, put -the XML and Python files in the tools/ncbi_blast_plus/ folder and add the XML -files to your tool_conf.xml as normal (and do the same in tool_conf.xml.sample -in order to run the unit tests). For example, use:: +the XML and Python files in the ``tools/ncbi_blast_plus/`` folder and add the +XML files to your ``tool_conf.xml`` as normal (and do the same in +``tool_conf.xml.sample`` in order to run the unit tests). For example, use:: <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> @@ -53,6 +53,7 @@ <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /> <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" /> + <tool file="ncbi_blast_plus/ncbi_dustmasker_wrapper.xml" /> <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" /> <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" /> <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" /> @@ -60,18 +61,21 @@ <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> </section> -You will also need to install 'blast_datatypes' from the Tool Shed. This -defines the BLAST XML file format ('blastxml') and protein and nucleotide -BLAST databases composite file formats ('blastdbp' and 'blastdbn'). +You will also need to install ``blast_datatypes`` from the Tool Shed. This +defines the BLAST XML file format (``blastxml``) and protein and nucleotide +BLAST databases composite file formats (``blastdbp`` and ``blastdbn``): + +* http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes As described above for an automated installation, you must also tell Galaxy -about any system level BLAST databases using the tool-data/blastdb*.loc files. +about any system level BLAST databases using the ``tool-data/blastdb*.loc`` +files. You must install the NCBI BLAST+ standalone tools somewhere on the system -path. Currently the unit tests are written using "BLAST 2.2.26+". +path. Currently the unit tests are written using "BLAST 2.2.28+". Run the functional tests (adjusting the section identifier to match your -tool_conf.xml.sample file):: +``tool_conf.xml.sample`` file):: ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools @@ -117,6 +121,21 @@ - Adopted standard MIT License. - Development moved to GitHub, https://github.com/peterjc/galaxy_blast - Updated citation information (Cock et al. 2013). +v0.0.21 - Use macros to simplify the XML wrappers. + - Added wrapper for dustmasker + - Enabled masking for makeblastdb + - Requires 'maskinfo-asn1' and 'maskinfo-asn1-binary' datatypes + defined in updated blast_datatypes on Galaxy ToolShed. + - Tests updated for BLAST+ 2.2.27 instead of BLAST+ 2.2.26 + - Now depends on package_blast_plus_2_2_27 in ToolShed +v0.0.22 - More use macros to simplify the wrappers + - Set number of threads via $GALAXY_SLOTS environment variable + - More descriptive default output names + - Tests require updated BLAST DB definitions (blast_datatypes v0.0.18) + - Pre-check for duplicate identifiers in makeblastdb wrapper. + - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27 + - Now depends on package_blast_plus_2_2_28 in ToolShed + - Extended tabular output includes 'salltitles' as column 25. ======= ====================================================================== @@ -140,11 +159,16 @@ For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use the following command from the GitHub repository root folder:: - $ ./ncbi_blast_plus/make_ncbi_blast_plus.sh + $ tools/ncbi_blast_plus/make_ncbi_blast_plus.sh This simplifies ensuring a consistent set of files is bundled each time, including all the relevant test files. +When updating the version of BLAST+, many of the sample data files used for +the unit tests must be regenerated. This script automates that task:: + + $ tools/ncbi_blast_plus/update_test_files.sh + Licence (MIT) =============
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Thu Dec 05 06:55:59 2013 -0500 @@ -31,7 +31,7 @@ ====== ============= =========================================== Column NCBI name Description ------ ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' + 13 sallseqid All subject Seq-id(s), separated by ';' 14 score Raw score 15 nident Number of identical matches 16 positive Number of positive-scoring matches @@ -43,6 +43,7 @@ 22 sseq Aligned part of subject sequence 23 qlen Query sequence length 24 slen Subject sequence length + 25 salltitles All subject titles, separated by '<>' ====== ============= =========================================== Most of these fields are given explicitly in the XML file, others some like @@ -63,7 +64,7 @@ import re if "-v" in sys.argv or "--version" in sys.argv: - print "v0.0.12" + print "v0.0.22" sys.exit(0) if sys.version_info[:2] >= ( 2, 5 ): @@ -89,11 +90,11 @@ if out_fmt == "std": extended = False elif out_fmt == "x22": - stop_err("Format argument x22 has been replaced with ext (extended 24 columns)") + stop_err("Format argument x22 has been replaced with ext (extended 25 columns)") elif out_fmt == "ext": extended = True else: - stop_err("Format argument should be std (12 column) or ext (extended 24 columns)") + stop_err("Format argument should be std (12 column) or ext (extended 25 columns), not: %r" % out_fmt) # get an iterable @@ -157,6 +158,11 @@ # <Hit_accession>Subject_1</Hit_accession> # #apparently depending on the parse_deflines switch + # + #Or, with BLAST 2.2.28+ can get this, + # <Hit_id>gnl|BL_ORD_ID|2</Hit_id> + # <Hit_def>chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence</Hit_def> + # <Hit_accession>2</Hit_accession> sseqid = hit.findtext("Hit_id").split(None,1)[0] hit_def = sseqid + " " + hit.findtext("Hit_def") if re_default_subject_id.match(sseqid) \ @@ -164,6 +170,11 @@ #Place holder ID, take the first word of the subject definition hit_def = hit.findtext("Hit_def") sseqid = hit_def.split(None,1)[0] + if sseqid.startswith("gnl|BL_ORD_ID|") \ + and sseqid == "gnl|BL_ORD_ID|" + hit.findtext("Hit_accession"): + #Alternative place holder ID, again take the first word of hit_def + hit_def = hit.findtext("Hit_def") + sseqid = hit_def.split(None,1)[0] # for every <Hsp> within <Hit> for hsp in hit.findall("Hit_hsps/Hsp"): nident = hsp.findtext("Hsp_identity") @@ -228,7 +239,11 @@ ] if extended: - sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(">")) + try: + sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(" >")) + salltitles = "<>".join(name.split(None,1)[1] for name in hit_def.split(" >")) + except IndexError as e: + stop_err("Problem splitting multuple hits?\n%r\n--> %s" % (hit_def, e)) #print hit_def, "-->", sallseqid positive = hsp.findtext("Hsp_positive") ppos = "%0.2f" % (100*float(positive)/float(length)) @@ -252,6 +267,7 @@ h_seq, str(qlen), str(slen), + salltitles, ]) #print "\t".join(values) outfile.write("\t".join(values) + "\n")
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Thu Dec 05 06:55:59 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.11"> +<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.22"> <description>Convert BLAST XML output to tabular</description> <version_command interpreter="python">blastxml_to_tabular.py --version</version_command> <command interpreter="python"> @@ -17,7 +17,7 @@ </param> </inputs> <outputs> - <data name="tabular_file" format="tabular" label="BLAST results as tabular" /> + <data name="tabular_file" format="tabular" label="$blastxml_file.display_name (as tabular)" /> </outputs> <requirements> </requirements> @@ -70,6 +70,16 @@ <!-- Note this has some white space differences from the actual blastp output --> <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" /> </test> + <test> + <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" /> + <param name="out_format" value="std" /> + <output name="tabular_file" file="blastn_arabidopsis.standard.tabular" ftype="tabular" /> + </test> + <test> + <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" /> + <param name="out_format" value="ext" /> + <output name="tabular_file" file="blastn_arabidopsis.extended.tabular" ftype="tabular" /> + </test> </tests> <help> @@ -104,13 +114,13 @@ but this takes longer to calculate. Most (but not all) of these columns are included by selecting the extended tabular output. The extra columns are included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 22 column tabular -BLAST output. This tool now uses this extended 24 column output by default. +workflow filtering steps that accept either the 12 or 25 column tabular +BLAST output. This tool now uses this extended 25 column output by default. ====== ============= =========================================== Column NCBI name Description ------ ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' + 13 sallseqid All subject Seq-id(s), separated by ';' 14 score Raw score 15 nident Number of identical matches 16 positive Number of positive-scoring matches @@ -122,6 +132,7 @@ 22 sseq Aligned part of subject sequence 23 qlen Query sequence length 24 slen Subject sequence length + 25 salltitles All subject title(s), separated by '<>' ====== ============= =========================================== Beware that the XML file (and thus the conversion) and the tabular output
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/check_no_duplicates.py Thu Dec 05 06:55:59 2013 -0500 @@ -0,0 +1,46 @@ +#!/usr/bin/env python +"""Check for duplicate sequence identifiers in FASTA files. + +This is run as a pre-check before makeblastdb, in order to avoid +a regression bug in BLAST+ 2.2.28 which fails to catch this. See: +http://blastedbio.blogspot.co.uk/2012/10/my-ids-not-good-enough-for-ncbi-blast.html + +This script takes one or more FASTA filenames as input, and +will return a non-zero error if any duplicate identifiers +are found. +""" +import sys +import os + +if "-v" in sys.argv or "--version" in sys.argv: + print("v0.0.22") + sys.exit(0) + +def stop_err(msg, error=1): + sys.stderr.write("%s\n" % msg) + sys.exit(error) + + +identifiers = set() +files = 0 +for filename in sys.argv[1:]: + if not os.path.isfile(filename): + stop_err("Missing FASTA file %r" % filename, 2) + files += 1 + handle = open(filename) + for line in handle: + if line.startswith(">"): + #The split will also take care of the new line character, + #e.g. ">test\n" and ">test description here\n" both give "test" + seq_id = line[1:].split(None, 1)[0] + if seq_id in identifiers: + handle.close() + stop_err("Repeated identifiers, e.g. %r" % seq_id, 1) + identifiers.add(seq_id) + handle.close() +if not files: + stop_err("No FASTA files given to check for duplicates", 3) +elif files == 1: + print("%i sequences" % len(identifiers)) +else: + print("%i sequences in %i FASTA files" % (len(identifiers), files))
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Thu Dec 05 06:55:59 2013 -0500 @@ -1,46 +1,16 @@ -<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.6"> +<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.22"> <description>Show BLAST database information from blastdbcmd</description> - <requirements> - <requirement type="binary">blastdbcmd</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> - </requirements> - <version_command>blastdbcmd -version</version_command> + <macros> + <token name="@BINARY@">blastdbcmd</token> + <import>ncbi_macros.xml</import> + </macros> + <expand macro="requirements" /> <command> blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- Suspect blastdbcmd sometimes fails to set error level --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + <expand macro="stdio" /> <inputs> - <conditional name="db_opts"> - <param name="db_type" type="select" label="Type of BLAST database"> - <option value="nucl" selected="True">Nucleotide</option> - <option value="prot">Protein</option> - </param> - <when value="nucl"> - <param name="database" type="select" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - </when> - <when value="prot"> - <param name="database" type="select" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - </when> - </conditional> + <expand macro="input_conditional_choose_db_type" /> </inputs> <outputs> <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> @@ -60,17 +30,6 @@ If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: -Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). -Galaxy tools and workflows for sequence analysis with applications -in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 - -Christiam Camacho et al. (2009). -BLAST+: architecture and applications. -BMC Bioinformatics. 15;10:421. -http://dx.doi.org/10.1186/1471-2105-10-421 - -This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus +@REFERENCES@ </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Thu Dec 05 06:55:59 2013 -0500 @@ -1,10 +1,10 @@ -<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.6"> +<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.22"> <description>Extract sequence(s) from BLAST database</description> - <requirements> - <requirement type="binary">blastdbcmd</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> - </requirements> - <version_command>blastdbcmd -version</version_command> + <macros> + <token name="@BINARY@">blastdbcmd</token> + <import>ncbi_macros.xml</import> + </macros> + <expand macro="requirements" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -47,39 +47,9 @@ | sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq" #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- Suspect blastdbcmd sometimes fails to set error level --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + <expand macro="stdio" /> <inputs> - <conditional name="db_opts"> - <param name="db_type" type="select" label="Type of BLAST database"> - <option value="nucl" selected="True">Nucleotide</option> - <option value="prot">Protein</option> - </param> - <when value="nucl"> - <param name="database" type="select" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - </when> - <when value="prot"> - <param name="database" type="select" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - </when> - </conditional> + <expand macro="input_conditional_choose_db_type" /> <conditional name="id_opts"> <param name="id_type" type="select" label="Type of identifier list"> <option value="file">From file</option> @@ -132,17 +102,6 @@ If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: -Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). -Galaxy tools and workflows for sequence analysis with applications -in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 - -Christiam Camacho et al. (2009). -BLAST+: architecture and applications. -BMC Bioinformatics. 15;10:421. -http://dx.doi.org/10.1186/1471-2105-10-421 - -This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus +@REFERENCES@ </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Dec 05 06:55:59 2013 -0500 @@ -1,91 +1,40 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.20"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.22"> <description>Search nucleotide database with nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> - <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> - <requirements> - <requirement type="binary">blastn</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> - </requirements> - <version_command>blastn -version</version_command> + <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> + <macros> + <token name="@BINARY@">blastn</token> + <import>ncbi_macros.xml</import> + </macros> + <expand macro="requirements" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces blastn -query "$query" -#if $db_opts.db_opts_selector == "db": - -db "${db_opts.database.fields.path}" -#elif $db_opts.db_opts_selector == "histdb": - -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" -#else: - -subject "$db_opts.subject" -#end if +@BLAST_DB_SUBJECT@ -task $blast_type -evalue $evalue_cutoff --out "$output1" -##Set the extended list here so if/when we add things, saved workflows are not affected -#if str($out_format)=="ext": - -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -#else: - -outfmt $out_format -#end if --num_threads 8 +@BLAST_OUTPUT@ +@THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -$adv_opts.filter_query $adv_opts.strand -## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string -## Note -max_target_seqs overrides -num_descriptions and -num_alignments -#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): --max_target_seqs $adv_opts.max_hits -#end if +@ADVANCED_OPTIONS@ #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): -perc_identity $adv_opts.identity_cutoff #end if -#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): --word_size $adv_opts.word_size -#end if $adv_opts.ungapped -$adv_opts.parse_deflines ## End of advanced options: #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + + <expand macro="stdio" /> + <inputs> <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">Locally installed BLAST database</option> - <option value="histdb">BLAST database from your history</option> - <option value="file">FASTA file from your history (see warning note below)</option> - </param> - <when value="db"> - <param name="database" type="select" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="histdb"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> - </when> - </conditional> + + <expand macro="input_conditional_nucleotide_db" /> + <param name="blast_type" type="select" display="radio" label="Type of BLAST"> <option value="megablast">megablast</option> <option value="blastn">blastn</option> @@ -96,60 +45,26 @@ <option value="vecscreen">vecscreen</option> --> </param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6">Tabular (standard 12 columns)</option> - <option value="ext" selected="True">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> + <expand macro="input_evalue" /> + <expand macro="input_out_format" /> + <expand macro="advanced_options"> + <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> + <expand macro="input_strand" /> + <expand macro="input_max_hits" /> + <param name="identity_cutoff" type="float" min="0" max="100" value="0" label="Percent identity cutoff (-perc_identity)" help="Use zero for no cutoff" /> + + <!-- I'd like word_size to be optional, with minimum 4 for blastn --> + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."> + <validator type="in_range" min="0" /> </param> - <when value="basic" /> - <when value="advanced"> - <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> - <param name="strand" type="select" label="Query strand(s) to search against database/subject"> - <option value="-strand both">Both</option> - <option value="-strand plus">Plus (forward)</option> - <option value="-strand minus">Minus (reverse complement)</option> - </param> - <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - <param name="identity_cutoff" type="float" min="0" max="100" value="0" label="Percent identity cutoff (-perc_identity)" help="Use zero for no cutoff" /> - <!-- I'd like word_size to be optional, with minimum 4 for blastn --> - <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."> - <validator type="in_range" min="0" /> - </param> - <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> - <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> - </when> - </conditional> + <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> + <expand macro="input_parse_deflines" /> + </expand> </inputs> <outputs> - <data name="output1" format="tabular" label="${blast_type.value_label} on ${on_string}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> + <data name="output1" format="tabular" label="${blast_type.value_label} $query.name vs @ON_DB_SUBJECT@"> + <expand macro="output_change_format" /> </data> </outputs> <tests> @@ -166,12 +81,7 @@ </tests> <help> -.. class:: warningmark - -**Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. - ------ +@SEARCH_TIME_WARNING@ **What it does** @@ -179,71 +89,11 @@ using the NCBI BLAST+ blastn command line tool. Algorithms include blastn, megablast, and discontiguous megablast. -.. class:: warningmark - -You can also search against a FASTA file of subject nucleotide -sequences. This is *not* advised because it is slower (only one -CPU is used), but more importantly gives e-values for pairwise -searches (very small e-values which will look overly signficiant). -In most cases you should instead turn the other FASTA file into a -database first using *makeblastdb* and search against that. +@FASTA_WARNING@ ----- -**Output format** - -Because Galaxy focuses on processing tabular data, the default output of this -tool is tabular. The standard BLAST+ tabular output contains 12 columns: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. Galaxy now uses this extended 24 column output by default. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -The third option is BLAST XML output, which is designed to be parsed by -another program, and is understood by some Galaxy tools. - -You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). -The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. -The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. -The two query anchored outputs show a multiple sequence alignment between the query and all the matches, -and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). +@OUTPUT_FORMAT@ ------- @@ -252,17 +102,6 @@ If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: -Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). -Galaxy tools and workflows for sequence analysis with applications -in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 - -Christiam Camacho et al. (2009). -BLAST+: architecture and applications. -BMC Bioinformatics. 15;10:421. -http://dx.doi.org/10.1186/1471-2105-10-421 - -This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus +@REFERENCES@ </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Dec 05 06:55:59 2013 -0500 @@ -1,156 +1,62 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.20"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.22"> <description>Search protein database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> - <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> - <requirements> - <requirement type="binary">blastp</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> - </requirements> - <version_command>blastp -version</version_command> + <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> + <macros> + <token name="@BINARY@">blastp</token> + <import>ncbi_macros.xml</import> + </macros> + <expand macro="requirements" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces blastp -query "$query" -#if $db_opts.db_opts_selector == "db": - -db "${db_opts.database.fields.path}" -#elif $db_opts.db_opts_selector == "histdb": - -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" -#else: - -subject "$db_opts.subject" -#end if +@BLAST_DB_SUBJECT@ -task $blast_type -evalue $evalue_cutoff --out "$output1" -##Set the extended list here so if/when we add things, saved workflows are not affected -#if str($out_format)=="ext": - -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -#else: - -outfmt $out_format -#end if --num_threads 8 +@BLAST_OUTPUT@ +@THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -$adv_opts.filter_query -matrix $adv_opts.matrix -## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string -## Note -max_target_seqs overrides -num_descriptions and -num_alignments -#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): --max_target_seqs $adv_opts.max_hits -#end if -#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): --word_size $adv_opts.word_size -#end if +@ADVANCED_OPTIONS@ ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped -$adv_opts.parse_deflines ## End of advanced options: #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + + <expand macro="stdio" /> + <inputs> <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">Locally installed BLAST database</option> - <option value="histdb">BLAST database from your history</option> - <option value="file">FASTA file from your history (see warning note below)</option> - </param> - <when value="db"> - <param name="database" type="select" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="histdb"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> - </when> - </conditional> + + <expand macro="input_conditional_protein_db" /> + <param name="blast_type" type="select" display="radio" label="Type of BLAST"> <option value="blastp">blastp</option> <option value="blastp-short">blastp-short</option> </param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6">Tabular (standard 12 columns)</option> - <option value="ext" selected="True">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> + <expand macro="input_evalue" /> + <expand macro="input_out_format" /> + <expand macro="advanced_options"> + <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> + <expand macro="input_filter_query_default_false" /> + <expand macro="input_scoring_matrix" /> + <expand macro="input_max_hits" /> + <expand macro="input_word_size" /> <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> + Can't use '-ungapped' on its own, error back is: + Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search + Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.' + <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> --> - </param> - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> - <param name="matrix" type="select" label="Scoring matrix"> - <option value="BLOSUM90">BLOSUM90</option> - <option value="BLOSUM80">BLOSUM80</option> - <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> - <option value="BLOSUM50">BLOSUM50</option> - <option value="BLOSUM45">BLOSUM45</option> - <option value="PAM250">PAM250</option> - <option value="PAM70">PAM70</option> - <option value="PAM30">PAM30</option> - </param> - <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - <!-- I'd like word_size to be optional, with minimum 2 for blastp --> - <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> - <validator type="in_range" min="0" /> - </param> - <!-- - Can't use '-ungapped' on its own, error back is: - Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search - Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.' - <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> - --> - <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> - </when> - </conditional> + <expand macro="input_parse_deflines" /> + </expand> </inputs> <outputs> - <data name="output1" format="tabular" label="${blast_type.value_label} on ${on_string}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> + <data name="output1" format="tabular" label="${blast_type.value_label} $query.name vs @ON_DB_SUBJECT@"> + <expand macro="output_change_format" /> </data> </outputs> <tests> @@ -216,83 +122,18 @@ </tests> <help> -.. class:: warningmark - -**Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. - ------ +@SEARCH_TIME_WARNING@ **What it does** Search a *protein database* using a *protein query*, using the NCBI BLAST+ blastp command line tool. -.. class:: warningmark - -You can also search against a FASTA file of subject protein -sequences. This is *not* advised because it is slower (only one -CPU is used), but more importantly gives e-values for pairwise -searches (very small e-values which will look overly signficiant). -In most cases you should instead turn the other FASTA file into a -database first using *makeblastdb* and search against that. +@FASTA_WARNING@ ----- -**Output format** - -Because Galaxy focuses on processing tabular data, the default output of this -tool is tabular. The standard BLAST+ tabular output contains 12 columns: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. Galaxy now uses this extended 24 column output by default. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -The third option is BLAST XML output, which is designed to be parsed by -another program, and is understood by some Galaxy tools. - -You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). -The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. -The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. -The two query anchored outputs show a multiple sequence alignment between the query and all the matches, -and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). +@OUTPUT_FORMAT@ ------- @@ -301,17 +142,6 @@ If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: -Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). -Galaxy tools and workflows for sequence analysis with applications -in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 - -Christiam Camacho et al. (2009). -BLAST+: architecture and applications. -BMC Bioinformatics. 15;10:421. -http://dx.doi.org/10.1186/1471-2105-10-421 - -This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus +@REFERENCES@ </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Dec 05 06:55:59 2013 -0500 @@ -1,173 +1,55 @@ -<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.19"> +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.22"> <description>Search protein database with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> - <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> - <requirements> - <requirement type="binary">blastx</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> - </requirements> - <version_command>blastx -version</version_command> + <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> + <macros> + <token name="@BINARY@">blastx</token> + <import>ncbi_macros.xml</import> + </macros> + <expand macro="requirements" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces blastx -query "$query" -#if $db_opts.db_opts_selector == "db": - -db "${db_opts.database.fields.path}" -#elif $db_opts.db_opts_selector == "histdb": - -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" -#else: - -subject "$db_opts.subject" -#end if +@BLAST_DB_SUBJECT@ -query_gencode $query_gencode -evalue $evalue_cutoff --out "$output1" -##Set the extended list here so if/when we add things, saved workflows are not affected -#if str($out_format)=="ext": - -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -#else: - -outfmt $out_format -#end if --num_threads 8 +@BLAST_OUTPUT@ +@THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -$adv_opts.filter_query $adv_opts.strand -matrix $adv_opts.matrix -## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string -## Note -max_target_seqs overrides -num_descriptions and -num_alignments -#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): --max_target_seqs $adv_opts.max_hits -#end if -#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): --word_size $adv_opts.word_size -#end if +@ADVANCED_OPTIONS@ $adv_opts.ungapped -$adv_opts.parse_deflines ## End of advanced options: #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + + <expand macro="stdio" /> + <inputs> <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">Locally installed BLAST database</option> - <option value="histdb">BLAST database from your history</option> - <option value="file">FASTA file from your history (see warning note below)</option> - </param> - <when value="db"> - <param name="database" type="select" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="histdb"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> - </when> - </conditional> - <param name="query_gencode" type="select" label="Query genetic code"> - <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> - <option value="1" select="True">1. Standard</option> - <option value="2">2. Vertebrate Mitochondrial</option> - <option value="3">3. Yeast Mitochondrial</option> - <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> - <option value="5">5. Invertebrate Mitochondrial</option> - <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> - <option value="9">9. Echinoderm Mitochondrial</option> - <option value="10">10. Euplotid Nuclear</option> - <option value="11">11. Bacteria and Archaea</option> - <option value="12">12. Alternative Yeast Nuclear</option> - <option value="13">13. Ascidian Mitochondrial</option> - <option value="14">14. Flatworm Mitochondrial</option> - <option value="15">15. Blepharisma Macronuclear</option> - <option value="16">16. Chlorophycean Mitochondrial Code</option> - <option value="21">21. Trematode Mitochondrial Code</option> - <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> - <option value="23">23. Thraustochytrium Mitochondrial Code</option> - <option value="24">24. Pterobranchia mitochondrial code</option> - </param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6">Tabular (standard 12 columns)</option> - <option value="ext" selected="True">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> - <param name="strand" type="select" label="Query strand(s) to search against database/subject"> - <option value="-strand both">Both</option> - <option value="-strand plus">Plus (forward)</option> - <option value="-strand minus">Minus (reverse complement)</option> - </param> - <param name="matrix" type="select" label="Scoring matrix"> - <option value="BLOSUM90">BLOSUM90</option> - <option value="BLOSUM80">BLOSUM80</option> - <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> - <option value="BLOSUM50">BLOSUM50</option> - <option value="BLOSUM45">BLOSUM45</option> - <option value="PAM250">PAM250</option> - <option value="PAM70">PAM70</option> - <option value="PAM30">PAM30</option> - </param> - <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - <!-- I'd like word_size to be optional, with minimum 2 for blastx --> - <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> - <validator type="in_range" min="0" /> - </param> - <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> - <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> - </when> - </conditional> + + <expand macro="input_conditional_protein_db" /> + <expand macro="input_query_gencode" /> + <expand macro="input_evalue" /> + + <expand macro="input_out_format" /> + <expand macro="advanced_options"> + <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> + <expand macro="input_filter_query_default_true" /> + <expand macro="input_strand" /> + <expand macro="input_scoring_matrix" /> + <expand macro="input_max_hits" /> + <expand macro="input_word_size" /> + <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> + <expand macro="input_parse_deflines" /> + </expand> </inputs> <outputs> - <data name="output1" format="tabular" label="blastx on ${on_string}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> + <data name="output1" format="tabular" label="blastx $query.name vs @ON_DB_SUBJECT@"> + <expand macro="output_change_format" /> </data> </outputs> <tests> @@ -204,83 +86,18 @@ </tests> <help> -.. class:: warningmark - -**Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. - ------ +@SEARCH_TIME_WARNING@ **What it does** Search a *protein database* using a *translated nucleotide query*, using the NCBI BLAST+ blastx command line tool. -.. class:: warningmark - -You can also search against a FASTA file of subject protein -sequences. This is *not* advised because it is slower (only one -CPU is used), but more importantly gives e-values for pairwise -searches (very small e-values which will look overly signficiant). -In most cases you should instead turn the other FASTA file into a -database first using *makeblastdb* and search against that. +@FASTA_WARNING@ ----- -**Output format** - -Because Galaxy focuses on processing tabular data, the default output of this -tool is tabular. The standard BLAST+ tabular output contains 12 columns: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. Galaxy now uses this extended 24 column output by default. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -The third option is BLAST XML output, which is designed to be parsed by -another program, and is understood by some Galaxy tools. - -You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). -The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. -The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. -The two query anchored outputs show a multiple sequence alignment between the query and all the matches, -and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). +@OUTPUT_FORMAT@ ------- @@ -289,17 +106,6 @@ If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: -Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). -Galaxy tools and workflows for sequence analysis with applications -in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 - -Christiam Camacho et al. (2009). -BLAST+: architecture and applications. -BMC Bioinformatics. 15;10:421. -http://dx.doi.org/10.1186/1471-2105-10-421 - -This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus +@REFERENCES@ </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Thu Dec 05 06:55:59 2013 -0500 @@ -0,0 +1,101 @@ +<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.0.22"> + <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo --> + <description>masks low complexity regions</description> + <macros> + <token name="@BINARY@">dustmasker</token> + <import>ncbi_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +dustmasker +#if $db_opts.db_opts_selector == "db": + -in "${db_opts.database.fields.path}" -infmt blastdb +#elif $db_opts.db_opts_selector == "histdb": + -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb +#else: + -in "$subject" -infmt fasta +#end if +-out "$outfile" +-window $window -level $level -linker $linker -outfmt $outformat + </command> + <expand macro="stdio" /> + <inputs> + <expand macro="input_conditional_nucleotide_db" /> + <param name="window" type="integer" value="64" label="DUST window length" /> + <param name="level" type="integer" value="20" label="DUST level" help="Score threshold for subwindows" /> + <param name="linker" type="integer" value="1" label="DUST linker" help="How close masked intervals should be to get merged together" /> + <param name="outformat" type="select" label="Output format"> +<!-- acclist and maskinfo_xml are listed as possible output formats in + "dustmasker -help", but were not recognized by NCBI BLAST up to + release 2.2.27+. Fixed in BLAST 2.2.28+. + seqloc_* formats are not very useful --> +<!-- <option value="acclist">acclist</option>--> + <option value="fasta">FASTA</option> + <option value="interval" selected="true">interval</option> + <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option> + <option value="maskinfo_asn1_text">maskinfo ASN.1 text</option> +<!-- <option value="maskinfo_xml">maskinfo_xml</option> + <option value="seqloc_asn1_bin">seqloc_asn1_bin</option> + <option value="seqloc_asn1_text">seqloc_asn1_text</option> + <option value="seqloc_xml">seqloc_xml</option>--> + </param> + </inputs> + <outputs> + <data name="outfile" format="interval" label="DUST Masked File"> + <change_format> + <when input="outformat" value="fasta" format="fasta" /> + <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> + <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="window" value="64" /> + <param name="level" value="20" /> + <param name="linker" value="1" /> + <param name="outformat" value="fasta" /> + <output name="outfile" file="dustmasker_three_human.fasta" /> + </test> + <test> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="window" value="64" /> + <param name="level" value="20" /> + <param name="linker" value="1" /> + <param name="outformat" value="maskinfo_asn1_bin" /> + <output name="outfile" file="dustmasker_three_human.maskinfo-asn1-binary" /> + </test> + <test> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="window" value="64" /> + <param name="level" value="20" /> + <param name="linker" value="1" /> + <param name="outformat" value="maskinfo_asn1_text" /> + <output name="outfile" file="dustmasker_three_human.maskinfo-asn1" /> + </test> + </tests> + <help> +**What it does** + +This tool identifies and masks out low complexity regions of a nucleotide database (or sequences in FASTA format) by using the symmetric DUST algorithm. + +If you select *maskinfo ASN.1* (binary or text) as output format, the output file can be used as masking data for NCBI BLAST+ makeblastdb tool. + +More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_. + +.. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers (a more specific paper covering this wrapper is planned): + +@REFERENCES@ + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Thu Dec 05 06:55:59 2013 -0500 @@ -0,0 +1,382 @@ +<macros> + <xml name="output_change_format"> + <change_format> + <when input="out_format" value="0" format="txt"/> + <when input="out_format" value="0 -html" format="html"/> + <when input="out_format" value="2" format="txt"/> + <when input="out_format" value="2 -html" format="html"/> + <when input="out_format" value="4" format="txt"/> + <when input="out_format" value="4 -html" format="html"/> + <when input="out_format" value="5" format="blastxml"/> + </change_format> + </xml> + <xml name="input_out_format"> + <param name="out_format" type="select" label="Output format"> + <option value="6">Tabular (standard 12 columns)</option> + <option value="ext" selected="True">Tabular (extended 25 columns)</option> + <option value="5">BLAST XML</option> + <option value="0">Pairwise text</option> + <option value="0 -html">Pairwise HTML</option> + <option value="2">Query-anchored text</option> + <option value="2 -html">Query-anchored HTML</option> + <option value="4">Flat query-anchored text</option> + <option value="4 -html">Flat query-anchored HTML</option> + <!-- + <option value="-outfmt 11">BLAST archive format (ASN.1)</option> + --> + </param> + </xml> + <xml name="input_scoring_matrix"> + <param name="matrix" type="select" label="Scoring matrix"> + <option value="BLOSUM90">BLOSUM90</option> + <option value="BLOSUM80">BLOSUM80</option> + <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> + <option value="BLOSUM50">BLOSUM50</option> + <option value="BLOSUM45">BLOSUM45</option> + <option value="PAM250">PAM250</option> + <option value="PAM70">PAM70</option> + <option value="PAM30">PAM30</option> + </param> + </xml> + <xml name="stdio"> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + </xml> + <xml name="input_query_gencode"> + <param name="query_gencode" type="select" label="Query genetic code"> + <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> + <option value="1" select="True">1. Standard</option> + <option value="2">2. Vertebrate Mitochondrial</option> + <option value="3">3. Yeast Mitochondrial</option> + <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> + <option value="5">5. Invertebrate Mitochondrial</option> + <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> + <option value="9">9. Echinoderm Mitochondrial</option> + <option value="10">10. Euplotid Nuclear</option> + <option value="11">11. Bacteria and Archaea</option> + <option value="12">12. Alternative Yeast Nuclear</option> + <option value="13">13. Ascidian Mitochondrial</option> + <option value="14">14. Flatworm Mitochondrial</option> + <option value="15">15. Blepharisma Macronuclear</option> + <option value="16">16. Chlorophycean Mitochondrial Code</option> + <option value="21">21. Trematode Mitochondrial Code</option> + <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> + <option value="23">23. Thraustochytrium Mitochondrial Code</option> + <option value="24">24. Pterobranchia mitochondrial code</option> + </param> + </xml> + <xml name="input_db_gencode"> + <param name="db_gencode" type="select" label="Database/subject genetic code"> + <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> + <option value="1" select="True">1. Standard</option> + <option value="2">2. Vertebrate Mitochondrial</option> + <option value="3">3. Yeast Mitochondrial</option> + <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> + <option value="5">5. Invertebrate Mitochondrial</option> + <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> + <option value="9">9. Echinoderm Mitochondrial</option> + <option value="10">10. Euplotid Nuclear</option> + <option value="11">11. Bacteria and Archaea</option> + <option value="12">12. Alternative Yeast Nuclear</option> + <option value="13">13. Ascidian Mitochondrial</option> + <option value="14">14. Flatworm Mitochondrial</option> + <option value="15">15. Blepharisma Macronuclear</option> + <option value="16">16. Chlorophycean Mitochondrial Code</option> + <option value="21">21. Trematode Mitochondrial Code</option> + <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> + <option value="23">23. Thraustochytrium Mitochondrial Code</option> + <option value="24">24. Pterobranchia mitochondrial code</option> + </param> + </xml> + <xml name="input_conditional_nucleotide_db"> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">Locally installed BLAST database</option> + <option value="histdb">BLAST database from your history</option> + <option value="file">FASTA file from your history (see warning note below)</option> + </param> + <when value="db"> + <param name="database" type="select" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="path" index="2"/> + </options> + </param> + <param name="histdb" type="hidden" value="" /> + <param name="subject" type="hidden" value="" /> + </when> + <when value="histdb"> + <param name="database" type="hidden" value="" /> + <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="histdb" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + </when> + </conditional> + </xml> + <xml name="input_conditional_protein_db"> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">Locally installed BLAST database</option> + <option value="histdb">BLAST database from your history</option> + <option value="file">FASTA file from your history (see warning note below)</option> + </param> + <when value="db"> + <param name="database" type="select" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="path" index="2"/> + </options> + </param> + <param name="histdb" type="hidden" value="" /> + <param name="subject" type="hidden" value="" /> + </when> + <when value="histdb"> + <param name="database" type="hidden" value="" /> + <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="histdb" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> + </when> + </conditional> + </xml> + <xml name="input_conditional_pssm"> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)"> + <option value="db" selected="True">Locally installed BLAST database</option> + <!-- TODO - define new datatype + <option value="histdb">BLAST protein domain database from your history</option> + --> + </param> + <when value="db"> + <param name="database" type="select" label="Protein domain database"> + <options from_file="blastdb_d.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="path" index="2"/> + </options> + </param> + <param name="histdb" type="hidden" value="" /> + <param name="subject" type="hidden" value="" /> + </when> + <!-- TODO - define new datatype + <when value="histdb"> + <param name="database" type="hidden" value="" /> + <param name="histdb" type="data" format="blastdbd" label="Protein domain database" /> + <param name="subject" type="hidden" value="" /> + </when> + --> + </conditional> + </xml> + <xml name="input_conditional_choose_db_type"> + <conditional name="db_opts"> + <param name="db_type" type="select" label="Type of BLAST database"> + <option value="nucl" selected="True">Nucleotide</option> + <option value="prot">Protein</option> + </param> + <when value="nucl"> + <param name="database" type="select" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="path" index="2"/> + </options> + </param> + </when> + <when value="prot"> + <param name="database" type="select" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="path" index="2"/> + </options> + </param> + </when> + </conditional> + </xml> + <xml name="input_parse_deflines"> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> + </xml> + <xml name="input_filter_query_default_false"> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> + </xml> + <xml name="input_filter_query_default_true"> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> + </xml> + <xml name="input_max_hits"> + <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> + </xml> + <xml name="input_evalue"> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> + </xml> + <xml name="input_word_size"> + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> + <validator type="in_range" min="0" /> + </param> + </xml> + <xml name="input_strand"> + <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <option value="-strand both">Both</option> + <option value="-strand plus">Plus (forward)</option> + <option value="-strand minus">Minus (reverse complement)</option> + </param> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="binary">@BINARY@</requirement> + <requirement type="package" version="2.2.28">blast+</requirement> + </requirements> + <version_command>@BINARY@ -version</version_command> + </xml> + <xml name="advanced_options"> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic" /> + <when value="advanced"> + <yield /> + </when> + </conditional> + </xml> + <token name="@THREADS@">-num_threads "\${GALAXY_SLOTS:-8}"</token> + <token name="@BLAST_DB_SUBJECT@"> +#if $db_opts.db_opts_selector == "db": + -db "${db_opts.database.fields.path}" +#elif $db_opts.db_opts_selector == "histdb": + -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" +#else: + -subject "$db_opts.subject" +#end if + </token> + <token name="@BLAST_OUTPUT@">-out "$output1" +##Set the extended list here so when we add things, saved workflows are not affected +#if str($out_format)=="ext": + -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles" +#else: + -outfmt $out_format +#end if + </token> + <token name="@ADVANCED_OPTIONS@">$adv_opts.filter_query +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if +#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): +-word_size $adv_opts.word_size +#end if +$adv_opts.parse_deflines + </token> + <!-- @ON_DB_SUBJECT@ is for use with @BLAST_DB_SUBJECT@ --> + <token name="@ON_DB_SUBJECT@">#if str($db_opts.db_opts_selector)=='db' +${db_opts.database} +#elif str($db_opts.db_opts_selector)=='histdb' +${db_opts.histdb.name} +#else +${db_opts.subject.name} +#end if</token> + <token name="@REFERENCES@"> +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus + </token> + <token name="@OUTPUT_FORMAT@">**Output format** + +Because Galaxy focuses on processing tabular data, the default output of this +tool is tabular. The standard BLAST+ tabular output contains 12 columns: + +====== ========= ============================================ +Column NCBI name Description +------ --------- -------------------------------------------- + 1 qseqid Query Seq-id (ID of your sequence) + 2 sseqid Subject Seq-id (ID of the database hit) + 3 pident Percentage of identical matches + 4 length Alignment length + 5 mismatch Number of mismatches + 6 gapopen Number of gap openings + 7 qstart Start of alignment in query + 8 qend End of alignment in query + 9 sstart Start of alignment in subject (database hit) + 10 send End of alignment in subject (database hit) + 11 evalue Expectation value (E-value) + 12 bitscore Bit score +====== ========= ============================================ + +The BLAST+ tools can optionally output additional columns of information, +but this takes longer to calculate. Most (but not all) of these columns are +included by selecting the extended tabular output. The extra columns are +included *after* the standard 12 columns. This is so that you can write +workflow filtering steps that accept either the 12 or 25 column tabular +BLAST output. Galaxy now uses this extended 25 column output by default. + +====== ============= =========================================== +Column NCBI name Description +------ ------------- ------------------------------------------- + 13 sallseqid All subject Seq-id(s), separated by ';' + 14 score Raw score + 15 nident Number of identical matches + 16 positive Number of positive-scoring matches + 17 gaps Total number of gaps + 18 ppos Percentage of positive-scoring matches + 19 qframe Query frame + 20 sframe Subject frame + 21 qseq Aligned part of query sequence + 22 sseq Aligned part of subject sequence + 23 qlen Query sequence length + 24 slen Subject sequence length + 25 salltitles All subject title(s), separated by '<>' +====== ============= =========================================== + +The third option is BLAST XML output, which is designed to be parsed by +another program, and is understood by some Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + </token> + <token name="@FASTA_WARNING@">.. class:: warningmark + +You can also search against a FASTA file of subject (target) +sequences. This is *not* advised because it is slower (only one +CPU is used), but more importantly gives e-values for pairwise +searches (very small e-values which will look overly signficiant). +In most cases you should instead turn the other FASTA file into a +database first using *makeblastdb* and search against that. + </token> + <token name="@SEARCH_TIME_WARNING@">.. class:: warningmark + +**Note**. Database searches may take a substantial amount of time. +For large input datasets it is advisable to allow overnight processing. + +----- + </token> +</macros>
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Dec 05 06:55:59 2013 -0500 @@ -1,11 +1,17 @@ -<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.5"> +<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.22"> <description>Make BLAST database</description> - <requirements> - <requirement type="binary">makeblastdb</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> - </requirements> - <version_command>makeblastdb -version</version_command> - <command> + <macros> + <token name="@BINARY@">makeblastdb</token> + <import>ncbi_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command interpreter="python">check_no_duplicates.py +##First check for duplicates (since BLAST+ 2.2.28 fails to do so) +##and abort (via the ampersand ampersand trick) if any are found. +#for $i in $in +"${i.file}" +#end for +&& makeblastdb -out "${os.path.join($outfile.extra_files_path,'blastdb')}" $parse_seqids $hash_index @@ -24,54 +30,55 @@ -title "BLAST Database" #end if -dbtype $dbtype -## #set $sep = '-mask_data ' -## #for $i in $mask_data -## $sep${i.file} -## #set $set = ', ' -## #end for +#set $mask_string = '' +#set $sep = '-mask_data ' +#for $i in $mask_data +#set $mask_string += $sep + str($i.file) +#set $sep = ',' +#end for +$mask_string +## #set $gi_mask_string = '' ## #set $sep = '-gi_mask -gi_mask_name ' ## #for $i in $gi_mask -## $sep${i.file} -## #set $set = ', ' -## #end for +## #set $gi_mask_string += $sep + str($i.file) +## #set $sep = ',' +## #end for +## $gi_mask_string ## #if $tax.select == 'id': ## -taxid $tax.id ## #else if $tax.select == 'map': ## -taxid_map $tax.map ## #end if +## -------------------------------------------------------------------- +## Capture the stdout log information to the primary file (plain text): +>> "$outfile" </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + <expand macro="stdio" /> <inputs> <param name="dbtype" type="select" display="radio" label="Molecule type of input"> <option value="prot">protein</option> <option value="nucl">nucleotide</option> </param> <!-- TODO Allow merging of existing BLAST databases (conditional on the database type) + NOTE Double check the new database would be self contained first <repeat name="in" title="BLAST or FASTA Database" min="1"> <param name="file" type="data" format="fasta,blastdbn,blastdbp" label="BLAST or FASTA database" /> </repeat> --> + <!-- TODO Switch this to using <param ... multiple="true" /> instead of <repeat> block? --> <repeat name="in" title="FASTA file" min="1"> <param name="file" type="data" format="fasta" /> </repeat> <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" /> <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="False" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" /> - <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values." help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." /> - + <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values" help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." /> <!-- SEQUENCE MASKING OPTIONS --> + <repeat name="mask_data" title="Masking data file"> + <param name="mask_data_file" type="data" format="maskinfo-asn1,maskinfo-asn1-binary" label="ASN.1 file containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> + </repeat> <!-- TODO - <repeat name="mask_data" title="Provide one or more files containing masking data"> - <param name="file" type="data" format="asnb" label="File containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> - </repeat> <repeat name="gi_mask" title="Create GI indexed masking data"> - <param name="file" type="data" format="asnb" label="Masking data output file" /> + <param name="gi_mask_file" type="data" format="asnb" label="Masking data output file" /> </repeat> --> @@ -104,6 +111,25 @@ </data> </outputs> <tests> + <!-- Note the (two line) PIN file is not reproducible run to run. + --> + <test> + <param name="dbtype" value="prot" /> + <param name="file" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="title" value="Just 4 human proteins" /> + <param name="parse_seqids" value="" /> + <param name="hash_index" value="true" /> + <output name="out_file" file="four_human_proteins.fasta.log" ftype="blastdbp" lines_diff="6"> + <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" /> + <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" /> + <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" /> + <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" /> + <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" /> + <extra_files type="file" value="four_human_proteins.fasta.phi" name="blastdb.phi" /> + <extra_files type="file" value="four_human_proteins.fasta.psd" name="blastdb.psd" /> + <extra_files type="file" value="four_human_proteins.fasta.psi" name="blastdb.psi" /> + </output> + </test> </tests> <help> **What it does** @@ -127,17 +153,6 @@ If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: -Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). -Galaxy tools and workflows for sequence analysis with applications -in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 - -Christiam Camacho et al. (2009). -BLAST+: architecture and applications. -BMC Bioinformatics. 15;10:421. -http://dx.doi.org/10.1186/1471-2105-10-421 - -This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus +@REFERENCES@ </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Thu Dec 05 06:55:59 2013 -0500 @@ -1,12 +1,12 @@ -<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.0.4"> +<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.0.22"> <description>Search protein domain database (PSSMs) with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> - <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> - <requirements> - <requirement type="binary">rpsblast</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> - </requirements> - <version_command>rpsblast -version</version_command> + <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> + <macros> + <token name="@BINARY@">deltablast</token> + <import>ncbi_macros.xml</import> + </macros> + <expand macro="requirements" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -18,121 +18,43 @@ -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" #end if -evalue $evalue_cutoff --out "$output1" -##Set the extended list here so if/when we add things, saved workflows are not affected -#if str($out_format)=="ext": - -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -#else: - -outfmt $out_format -#end if --num_threads 8 +@BLAST_OUTPUT@ +@THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -$adv_opts.filter_query -## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string -## Note -max_target_seqs overrides -num_descriptions and -num_alignments -#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): --max_target_seqs $adv_opts.max_hits -#end if -#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): --word_size $adv_opts.word_size -#end if -$adv_opts.parse_deflines +@ADVANCED_OPTIONS@ ## End of advanced options: #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + + <expand macro="stdio" /> + <inputs> <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)"> - <option value="db" selected="True">Locally installed BLAST database</option> - <!-- TODO - define new datatype - <option value="histdb">BLAST protein domain database from your history</option> - --> - </param> - <when value="db"> - <param name="database" type="select" label="Protein domain database"> - <options from_file="blastdb_d.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="hidden" value="" /> - </when> - <!-- TODO - define new datatype - <when value="histdb"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbd" label="Protein domain database" /> - <param name="subject" type="hidden" value="" /> - </when> - --> - </conditional> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6">Tabular (standard 12 columns)</option> - <option value="ext" selected="True">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> - <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - <!-- I'd like word_size to be optional, with minimum 2 for rpsblast --> - <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> - <validator type="in_range" min="0" /> - </param> - <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> - </when> - </conditional> + + <expand macro="input_conditional_pssm" /> + + <expand macro="input_evalue" /> + + <expand macro="input_out_format" /> + + <expand macro="advanced_options"> + <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> + <expand macro="input_filter_query_default_false" /> + <expand macro="input_max_hits" /> + <expand macro="input_word_size" /> + <expand macro="input_parse_deflines" /> + </expand> </inputs> <outputs> <data name="output1" format="tabular" label="rpsblast on ${on_string}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> + + <expand macro="output_change_format" /> + </data> </outputs> <help> -.. class:: warningmark - -**Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. - ------ +@SEARCH_TIME_WARNING@ **What it does** @@ -171,60 +93,7 @@ ----- -**Output format** - -Because Galaxy focuses on processing tabular data, the default output of this -tool is tabular. The standard BLAST+ tabular output contains 12 columns: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. Galaxy now uses this extended 24 column output by default. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -The third option is BLAST XML output, which is designed to be parsed by -another program, and is understood by some Galaxy tools. - -You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). -The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. -The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. -The two query anchored outputs show a multiple sequence alignment between the query and all the matches, -and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). +@OUTPUT_FORMAT@ ------- @@ -233,17 +102,6 @@ If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: -Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). -Galaxy tools and workflows for sequence analysis with applications -in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 - -Christiam Camacho et al. (2009). -BLAST+: architecture and applications. -BMC Bioinformatics. 15;10:421. -http://dx.doi.org/10.1186/1471-2105-10-421 - -This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus +@REFERENCES@ </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Thu Dec 05 06:55:59 2013 -0500 @@ -1,12 +1,12 @@ -<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.4"> +<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.22"> <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> - <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> - <requirements> - <requirement type="binary">rpstblastn</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> - </requirements> - <version_command>rpstblastn -version</version_command> + <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> + <macros> + <token name="@BINARY@">rpstblastn</token> + <import>ncbi_macros.xml</import> + </macros> + <expand macro="requirements" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -18,122 +18,41 @@ -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" #end if -evalue $evalue_cutoff --out "$output1" -## Set the extended list here so if/when we add things, saved workflows are not affected -#if str($out_format)=="ext": - -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -#else: - -outfmt $out_format -#end if +@BLAST_OUTPUT@ ## rpstblastn does not support multiple threads up to release 2.2.27+. Added in BLAST 2.2.28+. ##-num_threads 8 #if $adv_opts.adv_opts_selector=="advanced": -$adv_opts.filter_query -## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string -## Note -max_target_seqs overrides -num_descriptions and -num_alignments -#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): --max_target_seqs $adv_opts.max_hits -#end if -#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): --word_size $adv_opts.word_size -#end if -$adv_opts.parse_deflines +@ADVANCED_OPTIONS@ ## End of advanced options: #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + <expand macro="stdio" /> <inputs> <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)"> - <option value="db" selected="True">Locally installed BLAST database</option> - <!-- TODO - define new datatype - <option value="histdb">BLAST protein domain database from your history</option> - --> - </param> - <when value="db"> - <param name="database" type="select" label="Protein domain database"> - <options from_file="blastdb_d.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="hidden" value="" /> - </when> - <!-- TODO - define new datatype - <when value="histdb"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbd" label="Protein domain database" /> - <param name="subject" type="hidden" value="" /> - </when> - --> - </conditional> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6">Tabular (standard 12 columns)</option> - <option value="ext" selected="True">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> - <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - <!-- I'd like word_size to be optional, with minimum 2 for rpsblast --> - <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> - <validator type="in_range" min="0" /> - </param> - <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> - </when> - </conditional> + + <expand macro="input_conditional_pssm" /> + + <expand macro="input_evalue" /> + + <expand macro="input_out_format" /> + + <expand macro="advanced_options"> + <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> + <expand macro="input_filter_query_default_false" /> + <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> + <expand macro="input_max_hits" /> + <expand macro="input_word_size" /> + <expand macro="input_parse_deflines" /> + </expand> </inputs> <outputs> <data name="output1" format="tabular" label="rpstblastn on ${on_string}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> + <expand macro="output_change_format" /> </data> </outputs> <help> -.. class:: warningmark - -**Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. - ------ +@SEARCH_TIME_WARNING@ **What it does** @@ -172,60 +91,7 @@ ----- -**Output format** - -Because Galaxy focuses on processing tabular data, the default output of this -tool is tabular. The standard BLAST+ tabular output contains 12 columns: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. Galaxy now uses this extended 24 column output by default. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -The third option is BLAST XML output, which is designed to be parsed by -another program, and is understood by some Galaxy tools. - -You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). -The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. -The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. -The two query anchored outputs show a multiple sequence alignment between the query and all the matches, -and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). +@OUTPUT_FORMAT@ ------- @@ -234,17 +100,6 @@ If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: -Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). -Galaxy tools and workflows for sequence analysis with applications -in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 - -Christiam Camacho et al. (2009). -BLAST+: architecture and applications. -BMC Bioinformatics. 15;10:421. -http://dx.doi.org/10.1186/1471-2105-10-421 - -This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus +@REFERENCES@ </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Dec 05 06:55:59 2013 -0500 @@ -1,173 +1,59 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.20"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.22"> <description>Search translated nucleotide database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> - <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> - <requirements> - <requirement type="binary">tblastn</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> - </requirements> - <version_command>tblastn -version</version_command> + <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> + <macros> + <token name="@BINARY@">tblastn</token> + <import>ncbi_macros.xml</import> + </macros> + <expand macro="requirements" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces tblastn -query "$query" -#if $db_opts.db_opts_selector == "db": - -db "${db_opts.database.fields.path}" -#elif $db_opts.db_opts_selector == "histdb": - -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" -#else: - -subject "$db_opts.subject" -#end if +@BLAST_DB_SUBJECT@ -evalue $evalue_cutoff --out "$output1" -##Set the extended list here so if/when we add things, saved workflows are not affected -#if str($out_format)=="ext": - -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -#else: - -outfmt $out_format -#end if --num_threads 8 +@BLAST_OUTPUT@ +@THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -db_gencode $adv_opts.db_gencode -$adv_opts.filter_query -matrix $adv_opts.matrix -## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string -## Note -max_target_seqs overrides -num_descriptions and -num_alignments -#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): --max_target_seqs $adv_opts.max_hits -#end if -#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): --word_size $adv_opts.word_size -#end if +@ADVANCED_OPTIONS@ ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped -$adv_opts.parse_deflines ## End of advanced options: #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + + <expand macro="stdio" /> + <inputs> <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">Locally installed BLAST database</option> - <option value="histdb">BLAST database from your history</option> - <option value="file">FASTA file from your history (see warning note below)</option> - </param> - <when value="db"> - <param name="database" type="select" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="histdb"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> - </when> - </conditional> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6">Tabular (standard 12 columns)</option> - <option value="ext" selected="True">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> + + <expand macro="input_conditional_nucleotide_db" /> + <expand macro="input_out_format" /> + <expand macro="input_evalue" /> + <expand macro="advanced_options"> + <expand macro="input_db_gencode" /> + + <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> + <expand macro="input_filter_query_default_true" /> + <expand macro="input_scoring_matrix" /> + <expand macro="input_max_hits" /> + <expand macro="input_word_size" /> <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> + Can't use '-ungapped' on its own, error back is: + Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search + Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.' + <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> --> - </param> - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - <param name="db_gencode" type="select" label="Database/subject genetic code"> - <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> - <option value="1" select="True">1. Standard</option> - <option value="2">2. Vertebrate Mitochondrial</option> - <option value="3">3. Yeast Mitochondrial</option> - <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> - <option value="5">5. Invertebrate Mitochondrial</option> - <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> - <option value="9">9. Echinoderm Mitochondrial</option> - <option value="10">10. Euplotid Nuclear</option> - <option value="11">11. Bacteria and Archaea</option> - <option value="12">12. Alternative Yeast Nuclear</option> - <option value="13">13. Ascidian Mitochondrial</option> - <option value="14">14. Flatworm Mitochondrial</option> - <option value="15">15. Blepharisma Macronuclear</option> - <option value="16">16. Chlorophycean Mitochondrial Code</option> - <option value="21">21. Trematode Mitochondrial Code</option> - <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> - <option value="23">23. Thraustochytrium Mitochondrial Code</option> - <option value="24">24. Pterobranchia mitochondrial code</option> - </param> - <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> - <param name="matrix" type="select" label="Scoring matrix"> - <option value="BLOSUM90">BLOSUM90</option> - <option value="BLOSUM80">BLOSUM80</option> - <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> - <option value="BLOSUM50">BLOSUM50</option> - <option value="BLOSUM45">BLOSUM45</option> - <option value="PAM250">PAM250</option> - <option value="PAM70">PAM70</option> - <option value="PAM30">PAM30</option> - </param> - <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - <!-- I'd like word_size to be optional, with minimum 2 for blastp --> - <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> - <validator type="in_range" min="0" /> - </param> - <!-- - Can't use '-ungapped' on its own, error back is: - Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search - Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.' - <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> - --> - <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> - </when> - </conditional> + <expand macro="input_parse_deflines" /> + </expand> </inputs> <outputs> - <data name="output1" format="tabular" label="tblastn on ${on_string}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> + <data name="output1" format="tabular" label="tblastn $query.name vs @ON_DB_SUBJECT@"> + <expand macro="output_change_format" /> </data> </outputs> <tests> @@ -250,83 +136,18 @@ </tests> <help> -.. class:: warningmark - -**Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. - ------ +@SEARCH_TIME_WARNING@ **What it does** Search a *translated nucleotide database* using a *protein query*, using the NCBI BLAST+ tblastn command line tool. -.. class:: warningmark - -You can also search against a FASTA file of subject nucleotide -sequences. This is *not* advised because it is slower (only one -CPU is used), but more importantly gives e-values for pairwise -searches (very small e-values which will look overly signficiant). -In most cases you should instead turn the other FASTA file into a -database first using *makeblastdb* and search against that. +@FASTA_WARNING@ ----- -**Output format** - -Because Galaxy focuses on processing tabular data, the default output of this -tool is tabular. The standard BLAST+ tabular output contains 12 columns: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. Galaxy now uses this extended 24 column output by default. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -The third option is BLAST XML output, which is designed to be parsed by -another program, and is understood by some Galaxy tools. - -You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). -The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. -The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. -The two query anchored outputs show a multiple sequence alignment between the query and all the matches, -and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). +@OUTPUT_FORMAT@ ------- @@ -335,17 +156,6 @@ If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: -Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). -Galaxy tools and workflows for sequence analysis with applications -in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 - -Christiam Camacho et al. (2009). -BLAST+: architecture and applications. -BMC Bioinformatics. 15;10:421. -http://dx.doi.org/10.1186/1471-2105-10-421 - -This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus +@REFERENCES@ </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Dec 05 06:55:59 2013 -0500 @@ -1,193 +1,59 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.20"> +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.22"> <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> - <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> - <requirements> - <requirement type="binary">tblastx</requirement> - <requirement type="package" version="2.2.26+">blast+</requirement> - </requirements> - <version_command>tblastx -version</version_command> + <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> + <macros> + <token name="@BINARY@">tblastx</token> + <import>ncbi_macros.xml</import> + </macros> + <expand macro="requirements" /> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces tblastx -query "$query" -#if $db_opts.db_opts_selector == "db": - -db "${db_opts.database.fields.path}" -#elif $db_opts.db_opts_selector == "histdb": - -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" -#else: - -subject "$db_opts.subject" -#end if +@BLAST_DB_SUBJECT@ -query_gencode $query_gencode -evalue $evalue_cutoff --out "$output1" -##Set the extended list here so if/when we add things, saved workflows are not affected -#if str($out_format)=="ext": - -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -#else: - -outfmt $out_format -#end if --num_threads 8 +@BLAST_OUTPUT@ +@THREADS@ #if $adv_opts.adv_opts_selector=="advanced": -db_gencode $adv_opts.db_gencode -$adv_opts.filter_query $adv_opts.strand -matrix $adv_opts.matrix ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments -#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): --max_target_seqs $adv_opts.max_hits -#end if -#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): --word_size $adv_opts.word_size -#end if -$adv_opts.parse_deflines +@ADVANCED_OPTIONS@ ## End of advanced options: #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> + + <expand macro="stdio" /> + <inputs> <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">Locally installed BLAST database</option> - <option value="histdb">BLAST database from your history</option> - <option value="file">FASTA file from your history (see warning note below)</option> - </param> - <when value="db"> - <param name="database" type="select" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="histdb"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="histdb" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> - </when> - </conditional> - <param name="query_gencode" type="select" label="Query genetic code"> - <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> - <option value="1" select="True">1. Standard</option> - <option value="2">2. Vertebrate Mitochondrial</option> - <option value="3">3. Yeast Mitochondrial</option> - <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> - <option value="5">5. Invertebrate Mitochondrial</option> - <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> - <option value="9">9. Echinoderm Mitochondrial</option> - <option value="10">10. Euplotid Nuclear</option> - <option value="11">11. Bacteria and Archaea</option> - <option value="12">12. Alternative Yeast Nuclear</option> - <option value="13">13. Ascidian Mitochondrial</option> - <option value="14">14. Flatworm Mitochondrial</option> - <option value="15">15. Blepharisma Macronuclear</option> - <option value="16">16. Chlorophycean Mitochondrial Code</option> - <option value="21">21. Trematode Mitochondrial Code</option> - <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> - <option value="23">23. Thraustochytrium Mitochondrial Code</option> - <option value="24">24. Pterobranchia mitochondrial code</option> - </param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6">Tabular (standard 12 columns)</option> - <option value="ext" selected="True">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - <param name="db_gencode" type="select" label="Database/subject genetic code"> - <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> - <option value="1" select="True">1. Standard</option> - <option value="2">2. Vertebrate Mitochondrial</option> - <option value="3">3. Yeast Mitochondrial</option> - <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> - <option value="5">5. Invertebrate Mitochondrial</option> - <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> - <option value="9">9. Echinoderm Mitochondrial</option> - <option value="10">10. Euplotid Nuclear</option> - <option value="11">11. Bacteria and Archaea</option> - <option value="12">12. Alternative Yeast Nuclear</option> - <option value="13">13. Ascidian Mitochondrial</option> - <option value="14">14. Flatworm Mitochondrial</option> - <option value="15">15. Blepharisma Macronuclear</option> - <option value="16">16. Chlorophycean Mitochondrial Code</option> - <option value="21">21. Trematode Mitochondrial Code</option> - <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> - <option value="23">23. Thraustochytrium Mitochondrial Code</option> - <option value="24">24. Pterobranchia mitochondrial code</option> - </param> - <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> - <param name="strand" type="select" label="Query strand(s) to search against database/subject"> - <option value="-strand both">Both</option> - <option value="-strand plus">Plus (forward)</option> - <option value="-strand minus">Minus (reverse complement)</option> - </param> - <param name="matrix" type="select" label="Scoring matrix"> - <option value="BLOSUM90">BLOSUM90</option> - <option value="BLOSUM80">BLOSUM80</option> - <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> - <option value="BLOSUM50">BLOSUM50</option> - <option value="BLOSUM45">BLOSUM45</option> - <option value="PAM250">PAM250</option> - <option value="PAM70">PAM70</option> - <option value="PAM30">PAM30</option> - </param> - <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - <!-- I'd like word_size to be optional, with minimum 2 for tblastx --> - <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> - <validator type="in_range" min="0" /> - </param> - <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> - </when> - </conditional> + + <expand macro="input_conditional_nucleotide_db" /> + <expand macro="input_query_gencode" /> + <expand macro="input_evalue" /> + + <expand macro="input_out_format" /> + <expand macro="advanced_options"> + <expand macro="input_db_gencode" /> + + <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> + <expand macro="input_filter_query_default_true" /> + <expand macro="input_strand" /> + <expand macro="input_scoring_matrix" /> + <expand macro="input_max_hits" /> + <!-- I'd like word_size to be optional, with minimum 2 for tblastx --> + <expand macro="input_word_size" /> + <expand macro="input_parse_deflines" /> + </expand> </inputs> <outputs> - <data name="output1" format="tabular" label="tblastx on ${on_string}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> + <data name="output1" format="tabular" label="tblastx $query.name vs @ON_DB_SUBJECT@"> + <expand macro="output_change_format" /> </data> </outputs> <tests> @@ -204,83 +70,18 @@ </tests> <help> -.. class:: warningmark - -**Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. - ------ +@SEARCH_TIME_WARNING@ **What it does** Search a *translated nucleotide database* using a *protein query*, using the NCBI BLAST+ tblastx command line tool. -.. class:: warningmark - -You can also search against a FASTA file of subject nucleotide -sequences. This is *not* advised because it is slower (only one -CPU is used), but more importantly gives e-values for pairwise -searches (very small e-values which will look overly signficiant). -In most cases you should instead turn the other FASTA file into a -database first using *makeblastdb* and search against that. +@FASTA_WARNING@ ----- -**Output format** - -Because Galaxy focuses on processing tabular data, the default output of this -tool is tabular. The standard BLAST+ tabular output contains 12 columns: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. Galaxy now uses this extended 24 column output by default. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -The third option is BLAST XML output, which is designed to be parsed by -another program, and is understood by some Galaxy tools. - -You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). -The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. -The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. -The two query anchored outputs show a multiple sequence alignment between the query and all the matches, -and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). +@OUTPUT_FORMAT@ ------- @@ -289,17 +90,6 @@ If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: -Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). -Galaxy tools and workflows for sequence analysis with applications -in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 - -Christiam Camacho et al. (2009). -BLAST+: architecture and applications. -BMC Bioinformatics. 15;10:421. -http://dx.doi.org/10.1186/1471-2105-10-421 - -This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus +@REFERENCES@ </help> </tool>
--- a/tools/ncbi_blast_plus/repository_dependencies.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/repository_dependencies.xml Thu Dec 05 06:55:59 2013 -0500 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> - <repository changeset_revision="b3a3ba0c1d47" name="blast_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a04cf51612f1" name="blast_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> </repositories>
--- a/tools/ncbi_blast_plus/tool_dependencies.xml Mon Sep 23 06:14:13 2013 -0400 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Thu Dec 05 06:55:59 2013 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="blast+" version="2.2.26+"> - <repository changeset_revision="40c69b76b46e" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="blast+" version="2.2.28"> + <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>