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Remove blast tools and test data from the distribution, update tool_conf.xml.sample to reflect this.

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This commit is contained in:
Dannon Baker
2012-08-22 16:12:59 -04:00
parent 29d541c7be
commit 0b2e939d4d
11 changed files with 0 additions and 3109 deletions
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lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
-722
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@@ -1,722 +0,0 @@
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
<BlastOutput>
<BlastOutput_program>tblastn</BlastOutput_program>
<BlastOutput_version>TBLASTN 2.2.25+</BlastOutput_version>
<BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
<BlastOutput_db></BlastOutput_db>
<BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
<BlastOutput_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</BlastOutput_query-def>
<BlastOutput_query-len>406</BlastOutput_query-len>
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM80</Parameters_matrix>
<Parameters_expect>1e-10</Parameters_expect>
<Parameters_gap-open>10</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<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>732.392902459534</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>646.119739014374</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>151.343146656381</Hsp_bit-score>
<Hsp_score>342</Hsp_score>
<Hsp_evalue>1.39566684546685e-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>126.323929257285</Hsp_bit-score>
<Hsp_score>284</Hsp_score>
<Hsp_evalue>1.39566684546685e-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>229.420359574251</Hsp_bit-score>
<Hsp_score>523</Hsp_score>
<Hsp_evalue>9.84654801241353e-65</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>122.873002719478</Hsp_bit-score>
<Hsp_score>276</Hsp_score>
<Hsp_evalue>1.40732096096596e-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>57.7367643183824</Hsp_bit-score>
<Hsp_score>125</Hsp_score>
<Hsp_evalue>5.60065526485586e-13</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>658.197981896696</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>711.255977415469</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>626.708277239213</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>
test-data/tblastn_four_human_vs_rhodopsin.xml
-722
View File
@@ -1,722 +0,0 @@
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
<BlastOutput>
<BlastOutput_program>tblastn</BlastOutput_program>
<BlastOutput_version>TBLASTN 2.2.25+</BlastOutput_version>
<BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
<BlastOutput_db></BlastOutput_db>
<BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
<BlastOutput_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</BlastOutput_query-def>
<BlastOutput_query-len>406</BlastOutput_query-len>
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM80</Parameters_matrix>
<Parameters_expect>1e-10</Parameters_expect>
<Parameters_gap-open>10</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<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>732.392902459534</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>646.119739014374</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>151.343146656381</Hsp_bit-score>
<Hsp_score>342</Hsp_score>
<Hsp_evalue>1.39566684546685e-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>126.323929257285</Hsp_bit-score>
<Hsp_score>284</Hsp_score>
<Hsp_evalue>1.39566684546685e-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>229.420359574251</Hsp_bit-score>
<Hsp_score>523</Hsp_score>
<Hsp_evalue>9.84654801241353e-65</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>122.873002719478</Hsp_bit-score>
<Hsp_score>276</Hsp_score>
<Hsp_evalue>1.40732096096596e-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>57.7367643183824</Hsp_bit-score>
<Hsp_score>125</Hsp_score>
<Hsp_evalue>5.60065526485586e-13</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>658.197981896696</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>711.255977415469</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>626.708277239213</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>
tool_conf.xml.sample
-8
View File
@@ -244,14 +244,6 @@
<tool file="fastx_toolkit/fasta_nucleotide_changer.xml" />
<tool file="fastx_toolkit/fastx_collapser.xml" />
</section>
<section name="NCBI BLAST+" id="ncbi_blast_plus_tools">
<tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />
<tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
<tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" />
<tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
<tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />
<tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />
</section>
<section name="NGS: QC and manipulation" id="NGS_QC">
<label text="FastQC: fastq/sam/bam" id="fastqcsambam" />
tools/ncbi_blast_plus/blastxml_to_tabular.py
-254
View File
@@ -1,254 +0,0 @@
#!/usr/bin/env python
"""Convert a BLAST XML file to 12 column tabular output
Takes three command line options, input BLAST XML filename, output tabular
BLAST filename, output format (std for standard 12 columns, or ext for the
extended 24 columns offered in the BLAST+ wrappers).
The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart
qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which
mean:
====== ========= ============================================
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 additional columns offered in the Galaxy BLAST+ wrappers are:
====== ============= ===========================================
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
====== ============= ===========================================
Most of these fields are given explicitly in the XML file, others some like
the percentage identity and the number of gap openings must be calculated.
Be aware that the sequence in the extended tabular output or XML direct from
BLAST+ may or may not use XXXX masking on regions of low complexity. This
can throw the off the calculation of percentage identity and gap openings.
[In fact, both BLAST 2.2.24+ and 2.2.25+ have a subtle bug in this regard,
with these numbers changing depending on whether or not the low complexity
filter is used.]
This script attempts to produce identical output to what BLAST+ would have done.
However, check this with "diff -b ..." since BLAST+ sometimes includes an extra
space character (probably a bug).
"""
import sys
import re
if sys.version_info[:2] >= ( 2, 5 ):
import xml.etree.cElementTree as ElementTree
else:
from galaxy import eggs
import pkg_resources; pkg_resources.require( "elementtree" )
from elementtree import ElementTree
def stop_err( msg ):
sys.stderr.write("%s\n" % msg)
sys.exit(1)
#Parse Command Line
try:
in_file, out_file, out_fmt = sys.argv[1:]
except:
stop_err("Expect 3 arguments: input BLAST XML file, output tabular file, out format (std or ext)")
if out_fmt == "std":
extended = False
elif out_fmt == "x22":
stop_err("Format argument x22 has been replaced with ext (extended 24 columns)")
elif out_fmt == "ext":
extended = True
else:
stop_err("Format argument should be std (12 column) or ext (extended 24 columns)")
# get an iterable
try:
context = ElementTree.iterparse(in_file, events=("start", "end"))
except:
stop_err("Invalid data format.")
# turn it into an iterator
context = iter(context)
# get the root element
try:
event, root = context.next()
except:
stop_err( "Invalid data format." )
re_default_query_id = re.compile("^Query_\d+$")
assert re_default_query_id.match("Query_101")
assert not re_default_query_id.match("Query_101a")
assert not re_default_query_id.match("MyQuery_101")
re_default_subject_id = re.compile("^Subject_\d+$")
assert re_default_subject_id.match("Subject_1")
assert not re_default_subject_id.match("Subject_")
assert not re_default_subject_id.match("Subject_12a")
assert not re_default_subject_id.match("TheSubject_1")
outfile = open(out_file, 'w')
blast_program = None
for event, elem in context:
if event == "end" and elem.tag == "BlastOutput_program":
blast_program = elem.text
# for every <Iteration> tag
if event == "end" and elem.tag == "Iteration":
#Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA
# <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>
#
#Or, from BLAST 2.2.24+ run online
# <Iteration_query-ID>Query_1</Iteration_query-ID>
# <Iteration_query-def>Sample</Iteration_query-def>
# <Iteration_query-len>516</Iteration_query-len>
# <Iteration_hits>...
qseqid = elem.findtext("Iteration_query-ID")
if re_default_query_id.match(qseqid):
#Place holder ID, take the first word of the query definition
qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
qlen = int(elem.findtext("Iteration_query-len"))
# for every <Hit> within <Iteration>
for hit in elem.findall("Iteration_hits/Hit"):
#Expecting either this,
# <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
# <Hit_def>RecName: Full=Rhodopsin</Hit_def>
# <Hit_accession>P56514</Hit_accession>
#or,
# <Hit_id>Subject_1</Hit_id>
# <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def>
# <Hit_accession>Subject_1</Hit_accession>
#
#apparently depending on the parse_deflines switch
sseqid = hit.findtext("Hit_id").split(None,1)[0]
hit_def = sseqid + " " + hit.findtext("Hit_def")
if re_default_subject_id.match(sseqid) \
and sseqid == hit.findtext("Hit_accession"):
#Place holder ID, take the first word of the subject definition
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")
length = hsp.findtext("Hsp_align-len")
pident = "%0.2f" % (100*float(nident)/float(length))
q_seq = hsp.findtext("Hsp_qseq")
h_seq = hsp.findtext("Hsp_hseq")
m_seq = hsp.findtext("Hsp_midline")
assert len(q_seq) == len(h_seq) == len(m_seq) == int(length)
gapopen = str(len(q_seq.replace('-', ' ').split())-1 + \
len(h_seq.replace('-', ' ').split())-1)
mismatch = m_seq.count(' ') + m_seq.count('+') \
- q_seq.count('-') - h_seq.count('-')
#TODO - Remove this alternative mismatch calculation and test
#once satisifed there are no problems
expected_mismatch = len(q_seq) \
- sum(1 for q,h in zip(q_seq, h_seq) \
if q == h or q == "-" or h == "-")
xx = sum(1 for q,h in zip(q_seq, h_seq) if q=="X" and h=="X")
if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx):
stop_err("%s vs %s mismatches, expected %i <= %i <= %i" \
% (qseqid, sseqid, expected_mismatch - q_seq.count("X"),
int(mismatch), expected_mismatch))
#TODO - Remove this alternative identity calculation and test
#once satisifed there are no problems
expected_identity = sum(1 for q,h in zip(q_seq, h_seq) if q == h)
if not (expected_identity - xx <= int(nident) <= expected_identity + q_seq.count("X")):
stop_err("%s vs %s identities, expected %i <= %i <= %i" \
% (qseqid, sseqid, expected_identity, int(nident),
expected_identity + q_seq.count("X")))
evalue = hsp.findtext("Hsp_evalue")
if evalue == "0":
evalue = "0.0"
else:
evalue = "%0.0e" % float(evalue)
bitscore = float(hsp.findtext("Hsp_bit-score"))
if bitscore < 100:
#Seems to show one decimal place for lower scores
bitscore = "%0.1f" % bitscore
else:
#Note BLAST does not round to nearest int, it truncates
bitscore = "%i" % bitscore
values = [qseqid,
sseqid,
pident,
length, #hsp.findtext("Hsp_align-len")
str(mismatch),
gapopen,
hsp.findtext("Hsp_query-from"), #qstart,
hsp.findtext("Hsp_query-to"), #qend,
hsp.findtext("Hsp_hit-from"), #sstart,
hsp.findtext("Hsp_hit-to"), #send,
evalue, #hsp.findtext("Hsp_evalue") in scientific notation
bitscore, #hsp.findtext("Hsp_bit-score") rounded
]
if extended:
sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(">"))
#print hit_def, "-->", sallseqid
positive = hsp.findtext("Hsp_positive")
ppos = "%0.2f" % (100*float(positive)/float(length))
qframe = hsp.findtext("Hsp_query-frame")
sframe = hsp.findtext("Hsp_hit-frame")
if blast_program == "blastp":
#Probably a bug in BLASTP that they use 0 or 1 depending on format
if qframe == "0": qframe = "1"
if sframe == "0": sframe = "1"
slen = int(hit.findtext("Hit_len"))
values.extend([sallseqid,
hsp.findtext("Hsp_score"), #score,
nident,
positive,
hsp.findtext("Hsp_gaps"), #gaps,
ppos,
qframe,
sframe,
#NOTE - for blastp, XML shows original seq, tabular uses XXX masking
q_seq,
h_seq,
str(qlen),
str(slen),
])
#print "\t".join(values)
outfile.write("\t".join(values) + "\n")
# prevents ElementTree from growing large datastructure
root.clear()
elem.clear()
outfile.close()
tools/ncbi_blast_plus/blastxml_to_tabular.xml
-127
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@@ -1,127 +0,0 @@
<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.8">
<description>Convert BLAST XML output to tabular</description>
<command interpreter="python">
blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
</command>
<inputs>
<param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/>
<param name="out_format" type="select" label="Output format">
<option value="std" selected="True">Tabular (standard 12 columns)</option>
<option value="ext">Tabular (extended 24 columns)</option>
</param>
</inputs>
<outputs>
<data name="tabular_file" format="tabular" label="BLAST results as tabular" />
</outputs>
<requirements>
</requirements>
<tests>
<test>
<param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
<param name="out_format" value="std" />
<!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar -->
<output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.tabular" ftype="tabular" />
</test>
<test>
<param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
<param name="out_format" value="ext" />
<!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar -->
<output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" />
</test>
<test>
<param name="blastxml_file" value="blastp_sample.xml" ftype="blastxml" />
<param name="out_format" value="std" />
<!-- Note this has some white space differences from the actual blastp output -->
<output name="tabular_file" file="blastp_sample_converted.tabular" ftype="tabular" />
</test>
<test>
<param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
<param name="out_format" value="std" />
<!-- Note this has some white space differences from the actual blastx output -->
<output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.tabular" ftype="tabular" />
</test>
<test>
<param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
<param name="out_format" value="ext" />
<!-- Note this has some white space and XXXX masking differences from the actual blastx output -->
<output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.tabular" ftype="tabular" />
</test>
<test>
<param name="blastxml_file" value="blastx_sample.xml" ftype="blastxml" />
<param name="out_format" value="std" />
<!-- Note this has some white space differences from the actual blastx output -->
<output name="tabular_file" file="blastx_sample_converted.tabular" ftype="tabular" />
</test>
<test>
<param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
<param name="out_format" value="std" />
<!-- Note this has some white space differences from the actual blastp output -->
<output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_std.tabular" ftype="tabular" />
</test>
<test>
<param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
<param name="out_format" value="ext" />
<!-- 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>
</tests>
<help>
**What it does**
NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
formats including tabular and a more detailed XML format. A complex workflow
may need both the XML and the tabular output - but running BLAST twice is
slow and wasteful.
This tool takes the BLAST XML output and by default converts it into the
standard 12 column tabular equivalent:
====== ========= ============================================
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 22 column tabular
BLAST output.
====== ============= ===========================================
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
====== ============= ===========================================
Beware that the XML file (and thus the conversion) and the tabular output
direct from BLAST+ may differ in the presence of XXXX masking on regions
low complexity (columns 21 and 22), and thus also calculated figures like
the percentage idenity (column 3).
</help>
</tool>
tools/ncbi_blast_plus/hide_stderr.py
-49
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@@ -1,49 +0,0 @@
#!/usr/bin/env python
"""A simple script to redirect stderr to stdout when the return code is zero.
See https://bitbucket.org/galaxy/galaxy-central/issue/325/
Currently Galaxy ignores the return code from command line tools (even if it
is non-zero which by convention indicates an error) and treats any output on
stderr as an error (even though by convention stderr is used for errors or
warnings).
This script runs the given command line, capturing all stdout and stderr in
memory, and gets the return code. For a zero return code, any stderr (which
should be warnings only) is added to the stdout. That way Galaxy believes
everything is fine. For a non-zero return code, we output stdout as is, and
any stderr, plus the return code to ensure there is some output on stderr.
That way Galaxy treats this as an error.
Once issue 325 is fixed, this script will not be needed.
"""
import sys
import subprocess
#Avoid using shell=True when we call subprocess to ensure if the Python
#script is killed, so too is the BLAST process.
try:
words = []
for w in sys.argv[1:]:
if " " in w:
words.append('"%s"' % w)
else:
words.append(w)
cmd = " ".join(words)
child = subprocess.Popen(sys.argv[1:],
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
except Exception, err:
sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
sys.exit(1)
#Use .communicate as can get deadlocks with .wait(),
stdout, stderr = child.communicate()
return_code = child.returncode
if return_code:
sys.stdout.write(stdout)
sys.stderr.write(stderr)
sys.stderr.write("Return error code %i from command:\n" % return_code)
sys.stderr.write("%s\n" % cmd)
else:
sys.stdout.write(stdout)
sys.stdout.write(stderr)
tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
-211
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@@ -1,211 +0,0 @@
<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.11">
<description>Search nucleotide database with nucleotide query sequence(s)</description>
<!-- If job splitting is enabled, break up the query file into four -->
<parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
<version_command>blastn -version</version_command>
<command interpreter="python">hide_stderr.py
## 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}"
#else:
-subject "$db_opts.subject"
#end if
-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
#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 $adv_opts.max_hits
#end if
#if (str($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>
<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">BLAST Database</option>
<option value="file">FASTA file</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="subject" type="hidden" value="" />
</when>
<when value="file">
<param name="database" type="hidden" value="" />
<param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/>
</when>
</conditional>
<param name="blast_type" type="select" display="radio" label="Type of BLAST">
<option value="megablast">megablast</option>
<option value="blastn">blastn</option>
<option value="blastn-short">blastn-short</option>
<option value="dc-megablast">dc-megablast</option>
<!-- Using BLAST 2.2.24+ this gives an error:
BLAST engine error: Program type 'vecscreen' not supported
<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" selected="True">Tabular (standard 12 columns)</option>
<option value="ext">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 '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>
<!-- 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>
</inputs>
<outputs>
<data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}">
<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>
</outputs>
<requirements>
<requirement type="binary">blastn</requirement>
</requirements>
<help>
.. class:: warningmark
**Note**. Database searches may take a substantial amount of time.
For large input datasets it is advisable to allow overnight processing.
-----
**What it does**
Search a *nucleotide database* using a *nucleotide query*,
using the NCBI BLAST+ blastn command line tool.
Algorithms include blastn, megablast, and discontiguous megablast.
-----
**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.
====== ============= ===========================================
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).
-------
**References**
Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
</help>
</tool>
tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
-278
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@@ -1,278 +0,0 @@
<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.11">
<description>Search protein database with protein query sequence(s)</description>
<!-- If job splitting is enabled, break up the query file into four -->
<parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
<version_command>blastp -version</version_command>
<command interpreter="python">hide_stderr.py
## 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}"
#else:
-subject "$db_opts.subject"
#end if
-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
#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 $adv_opts.word_size
#end if
##Ungapped disabled for now - see comments below
##$adv_opts.ungapped
$adv_opts.parse_deflines
## End of advanced options:
#end if
</command>
<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">BLAST Database</option>
<option value="file">FASTA file</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="subject" type="hidden" value="" />
</when>
<when value="file">
<param name="database" type="hidden" value="" />
<param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/>
</when>
</conditional>
<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" selected="True">Tabular (standard 12 columns)</option>
<option value="ext">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" />
<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>
</inputs>
<outputs>
<data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}">
<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>
</outputs>
<requirements>
<requirement type="binary">blastp</requirement>
</requirements>
<tests>
<test>
<param name="query" value="four_human_proteins.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-8" />
<param name="blast_type" value="blastp" />
<param name="out_format" value="5" />
<param name="adv_opts_selector" value="advanced" />
<param name="filter_query" value="False" />
<param name="matrix" value="BLOSUM62" />
<param name="max_hits" value="0" />
<param name="word_size" value="0" />
<param name="parse_deflines" value="True" />
<output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
</test>
<test>
<param name="query" value="four_human_proteins.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-8" />
<param name="blast_type" value="blastp" />
<param name="out_format" value="6" />
<param name="adv_opts_selector" value="advanced" />
<param name="filter_query" value="False" />
<param name="matrix" value="BLOSUM62" />
<param name="max_hits" value="0" />
<param name="word_size" value="0" />
<param name="parse_deflines" value="True" />
<output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
</test>
<test>
<param name="query" value="four_human_proteins.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-8" />
<param name="blast_type" value="blastp" />
<param name="out_format" value="ext" />
<param name="adv_opts_selector" value="advanced" />
<param name="filter_query" value="False" />
<param name="matrix" value="BLOSUM62" />
<param name="max_hits" value="0" />
<param name="word_size" value="0" />
<param name="parse_deflines" value="True" />
<output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
</test>
<test>
<param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-8" />
<param name="blast_type" value="blastp" />
<param name="out_format" value="6" />
<param name="adv_opts_selector" value="basic" />
<output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" />
</test>
</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.
-----
**What it does**
Search a *protein database* using a *protein query*,
using the NCBI BLAST+ blastp command line tool.
-----
**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.
====== ============= ===========================================
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).
-------
**References**
Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005.
</help>
</tool>
tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
-242
View File
@@ -1,242 +0,0 @@
<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.11">
<description>Search protein database with translated nucleotide query sequence(s)</description>
<!-- If job splitting is enabled, break up the query file into four -->
<parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
<version_command>blastx -version</version_command>
<command interpreter="python">hide_stderr.py
## 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}"
#else:
-subject "$db_opts.subject"
#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
#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
$adv_opts.ungapped
$adv_opts.parse_deflines
## End of advanced options:
#end if
</command>
<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">BLAST Database</option>
<option value="file">FASTA file</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="subject" type="hidden" value="" />
</when>
<when value="file">
<param name="database" type="hidden" value="" />
<param name="subject" type="data" format="fasta" label="Protein 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" selected="True">Tabular (standard 12 columns)</option>
<option value="ext">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>
</inputs>
<outputs>
<data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}">
<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>
</outputs>
<requirements>
<requirement type="binary">blastx</requirement>
</requirements>
<tests>
<test>
<param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-10" />
<param name="out_format" value="5" />
<param name="adv_opts_selector" value="basic" />
<output name="output1" file="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
</test>
<test>
<param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-10" />
<param name="out_format" value="6" />
<param name="adv_opts_selector" value="basic" />
<output name="output1" file="blastx_rhodopsin_vs_four_human.tabular" ftype="tabular" />
</test>
<test>
<param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-10" />
<param name="out_format" value="ext" />
<param name="adv_opts_selector" value="basic" />
<output name="output1" file="blastx_rhodopsin_vs_four_human_ext.tabular" ftype="tabular" />
</test>
</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.
-----
**What it does**
Search a *protein database* using a *translated nucleotide query*,
using the NCBI BLAST+ blastx command line tool.
-----
**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.
====== ============= ===========================================
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).
-------
**References**
Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
</help>
</tool>
tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
-288
View File
@@ -1,288 +0,0 @@
<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.11">
<description>Search translated nucleotide database with protein query sequence(s)</description>
<!-- If job splitting is enabled, break up the query file into four -->
<parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
<version_command>tblastn -version</version_command>
<command interpreter="python">hide_stderr.py
## 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}"
#else:
-subject "$db_opts.subject"
#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
#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 $adv_opts.word_size
#end if
##Ungapped disabled for now - see comments below
##$adv_opts.ungapped
$adv_opts.parse_deflines
## End of advanced options:
#end if
</command>
<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">BLAST Database</option>
<option value="file">FASTA file</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="subject" type="hidden" value="" />
</when>
<when value="file">
<param name="database" 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" selected="True">Tabular (standard 12 columns)</option>
<option value="ext">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="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>
</inputs>
<outputs>
<data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}">
<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>
</outputs>
<requirements>
<requirement type="binary">tblastn</requirement>
</requirements>
<tests>
<test>
<param name="query" value="four_human_proteins.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-10" />
<param name="out_format" value="5" />
<param name="adv_opts_selector" value="advanced" />
<param name="filter_query" value="false" />
<param name="matrix" value="BLOSUM80" />
<param name="max_hits" value="0" />
<param name="word_size" value="0" />
<param name="parse_deflines" value="false" />
<output name="output1" file="tblastn_four_human_vs_rhodopsin.xml" ftype="blastxml" />
</test>
<test>
<param name="query" value="four_human_proteins.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-10" />
<param name="out_format" value="ext" />
<param name="adv_opts_selector" value="advanced" />
<param name="filter_query" value="false" />
<param name="matrix" value="BLOSUM80" />
<param name="max_hits" value="0" />
<param name="word_size" value="0" />
<param name="parse_deflines" value="false" />
<output name="output1" file="tblastn_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
</test>
<test>
<param name="query" value="four_human_proteins.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-10" />
<param name="out_format" value="6" />
<param name="adv_opts_selector" value="advanced" />
<param name="filter_query" value="false" />
<param name="matrix" value="BLOSUM80" />
<param name="max_hits" value="0" />
<param name="word_size" value="0" />
<param name="parse_deflines" value="false" />
<output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
</test>
<test>
<!-- Same as above, but parse deflines - on BLAST 2.2.25+ makes no difference -->
<param name="query" value="four_human_proteins.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-10" />
<param name="out_format" value="6" />
<param name="adv_opts_selector" value="advanced" />
<param name="filter_query" value="false" />
<param name="matrix" value="BLOSUM80" />
<param name="max_hits" value="0" />
<param name="word_size" value="0" />
<param name="parse_deflines" value="true" />
<output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
</test>
<test>
<param name="query" value="four_human_proteins.fasta" ftype="fasta" />
<param name="db_opts_selector" value="file" />
<param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
<param name="database" value="" />
<param name="evalue_cutoff" value="1e-10" />
<param name="out_format" value="0 -html" />
<param name="adv_opts_selector" value="advanced" />
<param name="filter_query" value="false" />
<param name="matrix" value="BLOSUM80" />
<param name="max_hits" value="0" />
<param name="word_size" value="0" />
<param name="parse_deflines" value="false" />
<output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" />
</test>
</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.
-----
**What it does**
Search a *translated nucleotide database* using a *protein query*,
using the NCBI BLAST+ tblastn command line tool.
-----
**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.
====== ============= ===========================================
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).
-------
**References**
Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
</help>
</tool>
tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
-208
View File
@@ -1,208 +0,0 @@
<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.11">
<description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>
<!-- If job splitting is enabled, break up the query file into four -->
<parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
<version_command>tblastx -version</version_command>
<command interpreter="python">hide_stderr.py
## 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}"
#else:
-subject "$db_opts.subject"
#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
#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
$adv_opts.parse_deflines
## End of advanced options:
#end if
</command>
<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">BLAST Database</option>
<option value="file">FASTA file</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="subject" type="hidden" value="" />
</when>
<when value="file">
<param name="database" 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" selected="True">Tabular (standard 12 columns)</option>
<option value="ext">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 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>
</inputs>
<outputs>
<data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}">
<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>
</outputs>
<requirements>
<requirement type="binary">tblastx</requirement>
</requirements>
<help>
.. class:: warningmark
**Note**. Database searches may take a substantial amount of time.
For large input datasets it is advisable to allow overnight processing.
-----
**What it does**
Search a *translated nucleotide database* using a *protein query*,
using the NCBI BLAST+ tblastx command line tool.
-----
**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.
====== ============= ===========================================
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).
-------
**References**
Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
</help>
</tool>