mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
More BLAST tests
This commit is contained in:
Kanwei Li
@@ -0,0 +1,722 @@
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<?xml version="1.0"?>
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<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
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<BlastOutput>
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<BlastOutput_program>tblastn</BlastOutput_program>
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<BlastOutput_version>TBLASTN 2.2.25+</BlastOutput_version>
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<BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
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<BlastOutput_db></BlastOutput_db>
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<BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
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<BlastOutput_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</BlastOutput_query-def>
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<BlastOutput_query-len>406</BlastOutput_query-len>
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<BlastOutput_param>
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<Parameters>
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<Parameters_matrix>BLOSUM80</Parameters_matrix>
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<Parameters_expect>1e-10</Parameters_expect>
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<Parameters_gap-open>10</Parameters_gap-open>
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<Parameters_gap-extend>1</Parameters_gap-extend>
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<Parameters_filter>F</Parameters_filter>
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</Parameters>
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</BlastOutput_param>
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<BlastOutput_iterations>
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<Iteration>
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<Iteration_iter-num>1</Iteration_iter-num>
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<Iteration_query-ID>Query_1</Iteration_query-ID>
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<Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
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<Iteration_query-len>406</Iteration_query-len>
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<Iteration_hits></Iteration_hits>
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<Iteration_stat>
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<Statistics>
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<Statistics_db-num>0</Statistics_db-num>
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<Statistics_db-len>0</Statistics_db-len>
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<Statistics_hsp-len>19</Statistics_hsp-len>
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<Statistics_eff-space>127710</Statistics_eff-space>
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<Statistics_kappa>0.071</Statistics_kappa>
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<Statistics_lambda>0.299</Statistics_lambda>
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<Statistics_entropy>0.27</Statistics_entropy>
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</Statistics>
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</Iteration_stat>
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<Iteration_message>No hits found</Iteration_message>
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</Iteration>
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<Iteration>
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<Iteration_iter-num>2</Iteration_iter-num>
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<Iteration_query-ID>Query_1</Iteration_query-ID>
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<Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
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<Iteration_query-len>406</Iteration_query-len>
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<Iteration_hits></Iteration_hits>
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<Iteration_stat>
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<Statistics>
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<Statistics_db-num>0</Statistics_db-num>
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<Statistics_db-len>0</Statistics_db-len>
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<Statistics_hsp-len>19</Statistics_hsp-len>
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<Statistics_eff-space>127710</Statistics_eff-space>
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<Statistics_kappa>0.071</Statistics_kappa>
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<Statistics_lambda>0.299</Statistics_lambda>
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<Statistics_entropy>0.27</Statistics_entropy>
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</Statistics>
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</Iteration_stat>
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<Iteration_message>No hits found</Iteration_message>
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</Iteration>
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<Iteration>
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<Iteration_iter-num>3</Iteration_iter-num>
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<Iteration_query-ID>Query_1</Iteration_query-ID>
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<Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
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<Iteration_query-len>406</Iteration_query-len>
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<Iteration_hits></Iteration_hits>
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||||
<Iteration_stat>
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||||
<Statistics>
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||||
<Statistics_db-num>0</Statistics_db-num>
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||||
<Statistics_db-len>0</Statistics_db-len>
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<Statistics_hsp-len>19</Statistics_hsp-len>
|
||||
<Statistics_eff-space>127710</Statistics_eff-space>
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||||
<Statistics_kappa>0.071</Statistics_kappa>
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||||
<Statistics_lambda>0.299</Statistics_lambda>
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||||
<Statistics_entropy>0.27</Statistics_entropy>
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</Statistics>
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</Iteration_stat>
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<Iteration_message>No hits found</Iteration_message>
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</Iteration>
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<Iteration>
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<Iteration_iter-num>4</Iteration_iter-num>
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<Iteration_query-ID>Query_1</Iteration_query-ID>
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<Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
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||||
<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>
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||||
</Statistics>
|
||||
</Iteration_stat>
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||||
<Iteration_message>No hits found</Iteration_message>
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||||
</Iteration>
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<Iteration>
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<Iteration_iter-num>5</Iteration_iter-num>
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<Iteration_query-ID>Query_1</Iteration_query-ID>
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<Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
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||||
<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>
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||||
</Statistics>
|
||||
</Iteration_stat>
|
||||
<Iteration_message>No hits found</Iteration_message>
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||||
</Iteration>
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<Iteration>
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<Iteration_iter-num>6</Iteration_iter-num>
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<Iteration_query-ID>Query_1</Iteration_query-ID>
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<Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
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||||
<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>
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||||
<Iteration_message>No hits found</Iteration_message>
|
||||
</Iteration>
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||||
<Iteration>
|
||||
<Iteration_iter-num>7</Iteration_iter-num>
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||||
<Iteration_query-ID>Query_2</Iteration_query-ID>
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||||
<Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
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||||
<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>
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||||
<Iteration_query-ID>Query_2</Iteration_query-ID>
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<Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
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||||
<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>
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||||
<Iteration>
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||||
<Iteration_iter-num>9</Iteration_iter-num>
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<Iteration_query-ID>Query_2</Iteration_query-ID>
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<Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
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||||
<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>
|
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<Iteration>
|
||||
<Iteration_iter-num>10</Iteration_iter-num>
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<Iteration_query-ID>Query_2</Iteration_query-ID>
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<Iteration_query-def>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
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<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>
|
||||
@@ -2,11 +2,12 @@
|
||||
"""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 x22 for the
|
||||
extended 22 columns offered in the BLAST+ wrappers).
|
||||
BLAST filename, output format (std for standard 12 columns, or ext for the
|
||||
extended 24 columns offered in the BLAST+ wrappers).
|
||||
|
||||
The 12 colums output are 'qseqid sseqid pident length mismatch gapopen qstart
|
||||
qend sstart send evalue bitscore' which mean:
|
||||
qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which
|
||||
mean:
|
||||
|
||||
====== ========= ============================================
|
||||
Column NCBI name Description
|
||||
@@ -25,7 +26,7 @@ Column NCBI name Description
|
||||
12 bitscore Bit score
|
||||
====== ========= ============================================
|
||||
|
||||
The additional columns are:
|
||||
The additional columns offered in the Galaxy BLAST+ wrappers are:
|
||||
|
||||
====== ============= ===========================================
|
||||
Column NCBI name Description
|
||||
@@ -40,20 +41,26 @@ Column NCBI name Description
|
||||
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 sutle bug in this regard,
|
||||
with these numbers changing depending on whether or not the low complexity
|
||||
filter is used.]
|
||||
|
||||
This script attempts to produce idential output to what BLAST+ would have done.
|
||||
However, check this with "diff -b ..." since BLAST+ sometimes includes an extra
|
||||
space character (probably a bug).
|
||||
|
||||
Beware that if using the extended output, the XML file contains the original
|
||||
aligned sequences, but the tabular output direct from BLAST+ may use XXXX
|
||||
masking on regions of low complexity (columns 21 and 22).
|
||||
"""
|
||||
import sys
|
||||
import re
|
||||
|
||||
assert sys.version_info[:2] >= ( 2, 4 )
|
||||
if sys.version_info[:2] >= ( 2, 5 ):
|
||||
@@ -69,14 +76,16 @@ def stop_err( msg ):
|
||||
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 x22)")
|
||||
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 x22 (extended 22 column)")
|
||||
stop_err("Format argument should be std (12 column) or ext (extended 24 columns)")
|
||||
|
||||
|
||||
# get an iterable
|
||||
@@ -92,6 +101,18 @@ try:
|
||||
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:
|
||||
@@ -99,10 +120,42 @@ for event, elem in context:
|
||||
blast_program = elem.text
|
||||
# for every <Iteration> tag
|
||||
if event == "end" and elem.tag == "Iteration":
|
||||
qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
|
||||
#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")
|
||||
@@ -164,7 +217,6 @@ for event, elem in context:
|
||||
]
|
||||
|
||||
if extended:
|
||||
hit_def = sseqid + " " + hit.findtext("Hit_def")
|
||||
sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(">"))
|
||||
#print hit_def, "-->", sallseqid
|
||||
positive = hsp.findtext("Hsp_positive")
|
||||
@@ -175,6 +227,7 @@ for event, elem in context:
|
||||
#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,
|
||||
@@ -185,7 +238,10 @@ for event, elem in context:
|
||||
sframe,
|
||||
#NOTE - for blastp, XML shows original seq, tabular uses XXX masking
|
||||
q_seq,
|
||||
h_seq])
|
||||
h_seq,
|
||||
str(qlen),
|
||||
str(slen),
|
||||
])
|
||||
#print "\t".join(values)
|
||||
outfile.write("\t".join(values) + "\n")
|
||||
# prevents ElementTree from growing large datastructure
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.6">
|
||||
<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
|
||||
@@ -7,7 +7,7 @@
|
||||
<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="x22">Tabular (extended 22 columns)</option>
|
||||
<option value="ext">Tabular (extended 24 columns)</option>
|
||||
</param>
|
||||
</inputs>
|
||||
<outputs>
|
||||
@@ -16,12 +16,36 @@
|
||||
<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 blastx output -->
|
||||
<!-- 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" />
|
||||
@@ -36,9 +60,9 @@
|
||||
</test>
|
||||
<test>
|
||||
<param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
|
||||
<param name="out_format" value="x22" />
|
||||
<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_x22.tabular" ftype="tabular" />
|
||||
<output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" />
|
||||
</test>
|
||||
</tests>
|
||||
<help>
|
||||
@@ -90,11 +114,14 @@ Column NCBI name Description
|
||||
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) contains the original
|
||||
aligned sequences, but the tabular output direct from BLAST+ may use XXXX
|
||||
masking on regions of low complexity (columns 21 and 22).
|
||||
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>
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.8">
|
||||
<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.9">
|
||||
<description>Search nucleotide database with nucleotide query sequence(s)</description>
|
||||
<command interpreter="python">hide_stderr.py
|
||||
## The command is a Cheetah template which allows some Python based syntax.
|
||||
@@ -13,7 +13,12 @@ blastn
|
||||
-task $blast_type
|
||||
-evalue $evalue_cutoff
|
||||
-out $output1
|
||||
-outfmt "$out_format"
|
||||
##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
|
||||
@@ -66,7 +71,7 @@ $adv_opts.parse_deflines
|
||||
<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="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq">Tabular (extended 22 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>
|
||||
@@ -121,8 +126,6 @@ $adv_opts.parse_deflines
|
||||
<requirements>
|
||||
<requirement type="binary">blastn</requirement>
|
||||
</requirements>
|
||||
<tests>
|
||||
</tests>
|
||||
<help>
|
||||
|
||||
.. class:: warningmark
|
||||
@@ -166,7 +169,7 @@ 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
|
||||
workflow filtering steps that accept either the 12 or 24 column tabular
|
||||
BLAST output.
|
||||
|
||||
====== ============= ===========================================
|
||||
@@ -182,6 +185,8 @@ Column NCBI name Description
|
||||
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
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.8">
|
||||
<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.9">
|
||||
<description>Search protein database with protein query sequence(s)</description>
|
||||
<command interpreter="python">hide_stderr.py
|
||||
## The command is a Cheetah template which allows some Python based syntax.
|
||||
@@ -13,7 +13,12 @@ blastp
|
||||
-task $blast_type
|
||||
-evalue $evalue_cutoff
|
||||
-out $output1
|
||||
-outfmt "$out_format"
|
||||
##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
|
||||
@@ -61,7 +66,7 @@ $adv_opts.parse_deflines
|
||||
<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="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq">Tabular (extended 22 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>
|
||||
@@ -127,6 +132,22 @@ $adv_opts.parse_deflines
|
||||
<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" />
|
||||
@@ -136,7 +157,7 @@ $adv_opts.parse_deflines
|
||||
<param name="blast_type" value="blastp" />
|
||||
<param name="out_format" value="6" />
|
||||
<param name="adv_opts_selector" value="advanced" />
|
||||
<param name="filter_query" value="True" />
|
||||
<param name="filter_query" value="False" />
|
||||
<param name="matrix" value="BLOSUM62" />
|
||||
<param name="max_hits" value="0" />
|
||||
<param name="word_size" value="0" />
|
||||
@@ -150,14 +171,14 @@ $adv_opts.parse_deflines
|
||||
<param name="database" value="" />
|
||||
<param name="evalue_cutoff" value="1e-8" />
|
||||
<param name="blast_type" value="blastp" />
|
||||
<param name="out_format" value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq" />
|
||||
<param name="out_format" value="ext" />
|
||||
<param name="adv_opts_selector" value="advanced" />
|
||||
<param name="filter_query" value="True" />
|
||||
<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_22c.tabular" ftype="tabular" />
|
||||
<output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
|
||||
</test>
|
||||
<test>
|
||||
<param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" />
|
||||
@@ -213,7 +234,7 @@ 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
|
||||
workflow filtering steps that accept either the 12 or 24 column tabular
|
||||
BLAST output.
|
||||
|
||||
====== ============= ===========================================
|
||||
@@ -229,6 +250,8 @@ Column NCBI name Description
|
||||
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
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.8">
|
||||
<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.9">
|
||||
<description>Search protein database with translated nucleotide query sequence(s)</description>
|
||||
<command interpreter="python">hide_stderr.py
|
||||
## The command is a Cheetah template which allows some Python based syntax.
|
||||
@@ -12,7 +12,12 @@ blastx
|
||||
#end if
|
||||
-evalue $evalue_cutoff
|
||||
-out $output1
|
||||
-outfmt "$out_format"
|
||||
##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
|
||||
@@ -56,7 +61,7 @@ $adv_opts.parse_deflines
|
||||
<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="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq">Tabular (extended 22 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>
|
||||
@@ -122,6 +127,36 @@ $adv_opts.parse_deflines
|
||||
<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>
|
||||
|
||||
@@ -165,7 +200,7 @@ 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
|
||||
workflow filtering steps that accept either the 12 or 24 column tabular
|
||||
BLAST output.
|
||||
|
||||
====== ============= ===========================================
|
||||
@@ -181,6 +216,8 @@ Column NCBI name Description
|
||||
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
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.8">
|
||||
<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.9">
|
||||
<description>Search translated nucleotide database with protein query sequence(s)</description>
|
||||
<command interpreter="python">hide_stderr.py
|
||||
## The command is a Cheetah template which allows some Python based syntax.
|
||||
@@ -12,7 +12,12 @@ tblastn
|
||||
#end if
|
||||
-evalue $evalue_cutoff
|
||||
-out $output1
|
||||
-outfmt "$out_format"
|
||||
##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
|
||||
@@ -56,7 +61,7 @@ $adv_opts.parse_deflines
|
||||
<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="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq">Tabular (extended 22 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>
|
||||
@@ -122,6 +127,36 @@ $adv_opts.parse_deflines
|
||||
<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" />
|
||||
@@ -196,7 +231,7 @@ 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
|
||||
workflow filtering steps that accept either the 12 or 24 column tabular
|
||||
BLAST output.
|
||||
|
||||
====== ============= ===========================================
|
||||
@@ -212,6 +247,8 @@ Column NCBI name Description
|
||||
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
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.8">
|
||||
<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.9">
|
||||
<description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>
|
||||
<command interpreter="python">hide_stderr.py
|
||||
## The command is a Cheetah template which allows some Python based syntax.
|
||||
@@ -12,7 +12,12 @@ tblastx
|
||||
#end if
|
||||
-evalue $evalue_cutoff
|
||||
-out $output1
|
||||
-outfmt "$out_format"
|
||||
##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
|
||||
@@ -55,7 +60,7 @@ $adv_opts.parse_deflines
|
||||
<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="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq">Tabular (extended 22 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>
|
||||
@@ -119,8 +124,6 @@ $adv_opts.parse_deflines
|
||||
<requirements>
|
||||
<requirement type="binary">tblastx</requirement>
|
||||
</requirements>
|
||||
<tests>
|
||||
</tests>
|
||||
<help>
|
||||
|
||||
.. class:: warningmark
|
||||
@@ -163,7 +166,7 @@ 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
|
||||
workflow filtering steps that accept either the 12 or 24 column tabular
|
||||
BLAST output.
|
||||
|
||||
====== ============= ===========================================
|
||||
@@ -179,6 +182,8 @@ Column NCBI name Description
|
||||
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
|
||||
|
||||
Reference in New Issue
Block a user