Mercurial > repos > devteam > ncbi_blast_plus
diff test-data/blastn_rhodopsin_vs_three_human.xml @ 21:7538e2bfcd41 draft
v0.2.00, for NCBI BLAST+ 2.5.0 via bioconda or tool_dependencies.xml
author | peterjc |
---|---|
date | Wed, 19 Apr 2017 05:27:19 -0400 |
parents | 577d9c12411a |
children | 31e517610e1f |
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--- a/test-data/blastn_rhodopsin_vs_three_human.xml Mon Nov 07 11:31:37 2016 -0500 +++ b/test-data/blastn_rhodopsin_vs_three_human.xml Wed Apr 19 05:27:19 2017 -0400 @@ -2,7 +2,7 @@ <!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 2.2.31+</BlastOutput_version> + <BlastOutput_version>BLASTN 2.5.0+</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></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> @@ -25,49 +25,9 @@ <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>15</Statistics_hsp-len> - <Statistics_eff-space>4933992</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_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>15</Statistics_hsp-len> - <Statistics_eff-space>4933992</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_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> <Hit> <Hit_num>1</Hit_num> - <Hit_id>Subject_3</Hit_id> + <Hit_id>ENA|BC112106|BC112106.1</Hit_id> <Hit_def>ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds</Hit_def> <Hit_accession>Subject_3</Hit_accession> <Hit_len>1213</Hit_len> @@ -98,8 +58,8 @@ <Statistics> <Statistics_db-num>0</Statistics_db-num> <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>15</Statistics_hsp-len> - <Statistics_eff-space>4933992</Statistics_eff-space> + <Statistics_hsp-len>16</Statistics_hsp-len> + <Statistics_eff-space>11015204</Statistics_eff-space> <Statistics_kappa>0.46</Statistics_kappa> <Statistics_lambda>1.28</Statistics_lambda> <Statistics_entropy>0.85</Statistics_entropy> @@ -107,47 +67,7 @@ </Iteration_stat> </Iteration> <Iteration> - <Iteration_iter-num>4</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>15</Statistics_hsp-len> - <Statistics_eff-space>7453579</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_message>No hits found</Iteration_message> -</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>15</Statistics_hsp-len> - <Statistics_eff-space>7453579</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_message>No hits found</Iteration_message> -</Iteration> -<Iteration> - <Iteration_iter-num>6</Iteration_iter-num> + <Iteration_iter-num>2</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> @@ -157,28 +77,8 @@ <Statistics> <Statistics_db-num>0</Statistics_db-num> <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>15</Statistics_hsp-len> - <Statistics_eff-space>7453579</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_message>No hits found</Iteration_message> -</Iteration> -<Iteration> - <Iteration_iter-num>7</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>16</Statistics_hsp-len> - <Statistics_eff-space>20482300</Statistics_eff-space> + <Statistics_eff-space>16645672</Statistics_eff-space> <Statistics_kappa>0.46</Statistics_kappa> <Statistics_lambda>1.28</Statistics_lambda> <Statistics_entropy>0.85</Statistics_entropy> @@ -187,34 +87,14 @@ <Iteration_message>No hits found</Iteration_message> </Iteration> <Iteration> - <Iteration_iter-num>8</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>16</Statistics_hsp-len> - <Statistics_eff-space>20482300</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_message>No hits found</Iteration_message> -</Iteration> -<Iteration> - <Iteration_iter-num>9</Iteration_iter-num> + <Iteration_iter-num>3</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_3</Hit_id> + <Hit_id>ENA|BC112106|BC112106.1</Hit_id> <Hit_def>ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds</Hit_def> <Hit_accession>Subject_3</Hit_accession> <Hit_len>1213</Hit_len> @@ -223,7 +103,7 @@ <Hsp_num>1</Hsp_num> <Hsp_bit-score>460.936</Hsp_bit-score> <Hsp_score>249</Hsp_score> - <Hsp_evalue>3.59583e-132</Hsp_evalue> + <Hsp_evalue>8.03308e-132</Hsp_evalue> <Hsp_query-from>1</Hsp_query-from> <Hsp_query-to>333</Hsp_query-to> <Hsp_hit-from>118</Hsp_hit-from> @@ -242,7 +122,7 @@ <Hsp_num>2</Hsp_num> <Hsp_bit-score>331.671</Hsp_bit-score> <Hsp_score>179</Hsp_score> - <Hsp_evalue>2.94161e-93</Hsp_evalue> + <Hsp_evalue>6.57155e-93</Hsp_evalue> <Hsp_query-from>3127</Hsp_query-from> <Hsp_query-to>3368</Hsp_query-to> <Hsp_hit-from>782</Hsp_hit-from> @@ -261,7 +141,7 @@ <Hsp_num>3</Hsp_num> <Hsp_bit-score>265.191</Hsp_bit-score> <Hsp_score>143</Hsp_score> - <Hsp_evalue>3.02604e-73</Hsp_evalue> + <Hsp_evalue>6.76016e-73</Hsp_evalue> <Hsp_query-from>1410</Hsp_query-from> <Hsp_query-to>1582</Hsp_query-to> <Hsp_hit-from>448</Hsp_hit-from> @@ -280,7 +160,7 @@ <Hsp_num>4</Hsp_num> <Hsp_bit-score>248.571</Hsp_bit-score> <Hsp_score>134</Hsp_score> - <Hsp_evalue>3.04752e-68</Hsp_evalue> + <Hsp_evalue>6.80816e-68</Hsp_evalue> <Hsp_query-from>2854</Hsp_query-from> <Hsp_query-to>3023</Hsp_query-to> <Hsp_hit-from>615</Hsp_hit-from> @@ -302,8 +182,8 @@ <Statistics> <Statistics_db-num>0</Statistics_db-num> <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>16</Statistics_hsp-len> - <Statistics_eff-space>20482300</Statistics_eff-space> + <Statistics_hsp-len>17</Statistics_hsp-len> + <Statistics_eff-space>45757404</Statistics_eff-space> <Statistics_kappa>0.46</Statistics_kappa> <Statistics_lambda>1.28</Statistics_lambda> <Statistics_entropy>0.85</Statistics_entropy> @@ -311,54 +191,14 @@ </Iteration_stat> </Iteration> <Iteration> - <Iteration_iter-num>10</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>15</Statistics_hsp-len> - <Statistics_eff-space>4628008</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_message>No hits found</Iteration_message> -</Iteration> -<Iteration> - <Iteration_iter-num>11</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>15</Statistics_hsp-len> - <Statistics_eff-space>4628008</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_message>No hits found</Iteration_message> -</Iteration> -<Iteration> - <Iteration_iter-num>12</Iteration_iter-num> + <Iteration_iter-num>4</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_3</Hit_id> + <Hit_id>ENA|BC112106|BC112106.1</Hit_id> <Hit_def>ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds</Hit_def> <Hit_accession>Subject_3</Hit_accession> <Hit_len>1213</Hit_len> @@ -389,8 +229,8 @@ <Statistics> <Statistics_db-num>0</Statistics_db-num> <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>15</Statistics_hsp-len> - <Statistics_eff-space>4628008</Statistics_eff-space> + <Statistics_hsp-len>16</Statistics_hsp-len> + <Statistics_eff-space>10331428</Statistics_eff-space> <Statistics_kappa>0.46</Statistics_kappa> <Statistics_lambda>1.28</Statistics_lambda> <Statistics_entropy>0.85</Statistics_entropy> @@ -398,54 +238,14 @@ </Iteration_stat> </Iteration> <Iteration> - <Iteration_iter-num>13</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>15</Statistics_hsp-len> - <Statistics_eff-space>4933992</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_message>No hits found</Iteration_message> -</Iteration> -<Iteration> - <Iteration_iter-num>14</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>15</Statistics_hsp-len> - <Statistics_eff-space>4933992</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_message>No hits found</Iteration_message> -</Iteration> -<Iteration> - <Iteration_iter-num>15</Iteration_iter-num> + <Iteration_iter-num>5</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_3</Hit_id> + <Hit_id>ENA|BC112106|BC112106.1</Hit_id> <Hit_def>ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds</Hit_def> <Hit_accession>Subject_3</Hit_accession> <Hit_len>1213</Hit_len> @@ -476,8 +276,8 @@ <Statistics> <Statistics_db-num>0</Statistics_db-num> <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>15</Statistics_hsp-len> - <Statistics_eff-space>4933992</Statistics_eff-space> + <Statistics_hsp-len>16</Statistics_hsp-len> + <Statistics_eff-space>11015204</Statistics_eff-space> <Statistics_kappa>0.46</Statistics_kappa> <Statistics_lambda>1.28</Statistics_lambda> <Statistics_entropy>0.85</Statistics_entropy> @@ -485,7 +285,7 @@ </Iteration_stat> </Iteration> <Iteration> - <Iteration_iter-num>16</Iteration_iter-num> + <Iteration_iter-num>6</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> @@ -495,48 +295,8 @@ <Statistics> <Statistics_db-num>0</Statistics_db-num> <Statistics_db-len>0</Statistics_db-len> - <Statistics_hsp-len>15</Statistics_hsp-len> - <Statistics_eff-space>6353949</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_message>No hits found</Iteration_message> -</Iteration> -<Iteration> - <Iteration_iter-num>17</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>15</Statistics_hsp-len> - <Statistics_eff-space>6353949</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_message>No hits found</Iteration_message> -</Iteration> -<Iteration> - <Iteration_iter-num>18</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>15</Statistics_hsp-len> - <Statistics_eff-space>6353949</Statistics_eff-space> + <Statistics_hsp-len>16</Statistics_hsp-len> + <Statistics_eff-space>14188352</Statistics_eff-space> <Statistics_kappa>0.46</Statistics_kappa> <Statistics_lambda>1.28</Statistics_lambda> <Statistics_entropy>0.85</Statistics_entropy>