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comparison test-data/blastn_arabidopsis.xml @ 11:4c4a0da938ff draft

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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.
author peterjc
date Thu, 05 Dec 2013 06:55:59 -0500
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10:70e7dcbf6573 11:4c4a0da938ff
1 <?xml version="1.0"?>
2 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
3 <BlastOutput>
4 <BlastOutput_program>blastn</BlastOutput_program>
5 <BlastOutput_version>BLASTN 2.2.28+</BlastOutput_version>
6 <BlastOutput_reference>Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), &quot;A greedy algorithm for aligning DNA sequences&quot;, J Comput Biol 2000; 7(1-2):203-14.</BlastOutput_reference>
7 <BlastOutput_db>/mnt/galaxy/galaxy-central/database/files/000/dataset_857_files/blastdb</BlastOutput_db>
8 <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
9 <BlastOutput_query-def>chunk_of_plant</BlastOutput_query-def>
10 <BlastOutput_query-len>630</BlastOutput_query-len>
11 <BlastOutput_param>
12 <Parameters>
13 <Parameters_expect>0.001</Parameters_expect>
14 <Parameters_sc-match>1</Parameters_sc-match>
15 <Parameters_sc-mismatch>-2</Parameters_sc-mismatch>
16 <Parameters_gap-open>0</Parameters_gap-open>
17 <Parameters_gap-extend>0</Parameters_gap-extend>
18 <Parameters_filter>L;m;</Parameters_filter>
19 </Parameters>
20 </BlastOutput_param>
21 <BlastOutput_iterations>
22 <Iteration>
23 <Iteration_iter-num>1</Iteration_iter-num>
24 <Iteration_query-ID>Query_1</Iteration_query-ID>
25 <Iteration_query-def>chunk_of_plant</Iteration_query-def>
26 <Iteration_query-len>630</Iteration_query-len>
27 <Iteration_hits>
28 <Hit>
29 <Hit_num>1</Hit_num>
30 <Hit_id>gnl|BL_ORD_ID|2</Hit_id>
31 <Hit_def>chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence</Hit_def>
32 <Hit_accession>2</Hit_accession>
33 <Hit_len>23459830</Hit_len>
34 <Hit_hsps>
35 <Hsp>
36 <Hsp_num>1</Hsp_num>
37 <Hsp_bit-score>1164.51</Hsp_bit-score>
38 <Hsp_score>630</Hsp_score>
39 <Hsp_evalue>0</Hsp_evalue>
40 <Hsp_query-from>1</Hsp_query-from>
41 <Hsp_query-to>630</Hsp_query-to>
42 <Hsp_hit-from>4341</Hsp_hit-from>
43 <Hsp_hit-to>4970</Hsp_hit-to>
44 <Hsp_query-frame>1</Hsp_query-frame>
45 <Hsp_hit-frame>1</Hsp_hit-frame>
46 <Hsp_identity>630</Hsp_identity>
47 <Hsp_positive>630</Hsp_positive>
48 <Hsp_gaps>0</Hsp_gaps>
49 <Hsp_align-len>630</Hsp_align-len>
50 <Hsp_qseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_qseq>
51 <Hsp_hseq>GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT</Hsp_hseq>
52 <Hsp_midline>||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>
53 </Hsp>
54 </Hit_hsps>
55 </Hit>
56 </Iteration_hits>
57 <Iteration_stat>
58 <Statistics>
59 <Statistics_db-num>5</Statistics_db-num>
60 <Statistics_db-len>119146348</Statistics_db-len>
61 <Statistics_hsp-len>26</Statistics_hsp-len>
62 <Statistics_eff-space>71964315672</Statistics_eff-space>
63 <Statistics_kappa>0.46</Statistics_kappa>
64 <Statistics_lambda>1.28</Statistics_lambda>
65 <Statistics_entropy>0.85</Statistics_entropy>
66 </Statistics>
67 </Iteration_stat>
68 </Iteration>
69 </BlastOutput_iterations>
70 </BlastOutput>
71