| Previous changeset 30:d724d9af93ee (2017-10-30) Next changeset 32:360352490a06 (2018-06-05) |
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Commit message:
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 16ef84e19ea373838bbfb921b9ef2cd4b02b8788-dirty |
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modified:
test-data/blastn_chimera_vs_rhodopsin_db.tabular test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular test-data/blastn_chimera_vs_three_human_max1.txt test-data/blastn_rhodopsin_vs_three_human.xml test-data/blastp_four_human_vs_rhodopsin.tabular test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_ext.tabular test-data/blastx_rhodopsin_vs_four_human.xml test-data/cd00003_and_cd00008.pin test-data/four_human_proteins.dbinfo.txt test-data/four_human_proteins.fasta.pin test-data/four_human_proteins_taxid.fasta.pin test-data/rhodopsin_nucs.dbinfo.txt test-data/rhodopsin_nucs.fasta.nin test-data/tblastn_four_human_vs_rhodopsin.html test-data/tblastn_four_human_vs_rhodopsin.xml test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular test-data/three_human_mRNA.dbinfo.txt test-data/three_human_mRNA.fasta.nin tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml tools/ncbi_blast_plus/ncbi_macros.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastn_chimera_vs_rhodopsin_db.tabular --- a/test-data/blastn_chimera_vs_rhodopsin_db.tabular Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastn_chimera_vs_rhodopsin_db.tabular Mon May 28 07:57:56 2018 -0400 |
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| @@ -1,8 +1,8 @@ -chimera NM_001009242 92.308 1014 78 0 8881 9894 34 1047 0.0 1441 -chimera GQ290312 91.527 956 81 0 8881 9836 4 959 0.0 1317 -chimera AB062417 87.586 1015 124 2 8881 9894 34 1047 0.0 1175 -chimera GQ290303 91.515 330 28 0 8881 9210 4 333 8.28e-130 455 -chimera GQ290303 91.358 243 19 2 9542 9783 3127 3368 1.46e-92 331 -chimera GQ290303 94.220 173 10 0 9208 9380 1410 1582 1.50e-72 265 -chimera GQ290303 92.941 170 12 0 9375 9544 2854 3023 1.51e-67 248 -chimera GQ290303 95.588 68 3 0 9781 9848 4222 4289 7.43e-26 110 +chimera NM_001009242.1 92.308 1014 78 0 8881 9894 34 1047 0.0 1441 +chimera GQ290312.1 91.527 956 81 0 8881 9836 4 959 0.0 1317 +chimera AB062417.1 87.586 1015 124 2 8881 9894 34 1047 0.0 1175 +chimera GQ290303.1 91.515 330 28 0 8881 9210 4 333 8.28e-130 455 +chimera GQ290303.1 91.358 243 19 2 9542 9783 3127 3368 1.46e-92 331 +chimera GQ290303.1 94.220 173 10 0 9208 9380 1410 1582 1.50e-72 265 +chimera GQ290303.1 92.941 170 12 0 9375 9544 2854 3023 1.51e-67 248 +chimera GQ290303.1 95.588 68 3 0 9781 9848 4222 4289 7.43e-26 110 |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular --- a/test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastn_chimera_vs_three_human_and_rhodopsin_db.tabular Mon May 28 07:57:56 2018 -0400 |
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| @@ -1,11 +1,11 @@ chimera ENA|AB011145|AB011145.1 100.000 4560 0 0 1 4560 121 4680 0.0 8421 chimera ENA|M10051|M10051.1 99.931 4331 3 0 4560 8890 60 4390 0.0 7982 chimera ENA|BC112106|BC112106.1 100.000 1093 0 0 8881 9973 121 1213 0.0 2019 -chimera NM_001009242 92.308 1014 78 0 8881 9894 34 1047 0.0 1441 -chimera GQ290312 91.527 956 81 0 8881 9836 4 959 0.0 1317 -chimera AB062417 87.586 1015 124 2 8881 9894 34 1047 0.0 1175 -chimera GQ290303 91.515 330 28 0 8881 9210 4 333 1.70e-129 455 -chimera GQ290303 91.358 243 19 2 9542 9783 3127 3368 2.98e-92 331 -chimera GQ290303 94.220 173 10 0 9208 9380 1410 1582 3.07e-72 265 -chimera GQ290303 92.941 170 12 0 9375 9544 2854 3023 3.09e-67 248 -chimera GQ290303 95.588 68 3 0 9781 9848 4222 4289 1.52e-25 110 +chimera NM_001009242.1 92.308 1014 78 0 8881 9894 34 1047 0.0 1441 +chimera GQ290312.1 91.527 956 81 0 8881 9836 4 959 0.0 1317 +chimera AB062417.1 87.586 1015 124 2 8881 9894 34 1047 0.0 1175 +chimera GQ290303.1 91.515 330 28 0 8881 9210 4 333 1.70e-129 455 +chimera GQ290303.1 91.358 243 19 2 9542 9783 3127 3368 2.98e-92 331 +chimera GQ290303.1 94.220 173 10 0 9208 9380 1410 1582 3.07e-72 265 +chimera GQ290303.1 92.941 170 12 0 9375 9544 2854 3023 3.09e-67 248 +chimera GQ290303.1 95.588 68 3 0 9781 9848 4222 4289 1.52e-25 110 |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastn_chimera_vs_three_human_max1.txt --- a/test-data/blastn_chimera_vs_three_human_max1.txt Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastn_chimera_vs_three_human_max1.txt Mon May 28 07:57:56 2018 -0400 |
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| @@ -1,4 +1,4 @@ -BLASTN 2.5.0+ +BLASTN 2.7.1+ Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb @@ -346,7 +346,7 @@ Database: Just 3 human mRNA sequences - Posted date: Dec 2, 2016 10:38 AM + Posted date: Oct 31, 2017 4:23 PM Number of letters in database: 10,732 Number of sequences in database: 3 |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastn_rhodopsin_vs_three_human.xml --- a/test-data/blastn_rhodopsin_vs_three_human.xml Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastn_rhodopsin_vs_three_human.xml Mon May 28 07:57:56 2018 -0400 |
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| @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastn</BlastOutput_program> - <BlastOutput_version>BLASTN 2.5.0+</BlastOutput_version> + <BlastOutput_version>BLASTN 2.7.1+</BlastOutput_version> <BlastOutput_reference>Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastp_four_human_vs_rhodopsin.tabular --- a/test-data/blastp_four_human_vs_rhodopsin.tabular Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin.tabular Mon May 28 07:57:56 2018 -0400 |
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| @@ -1,6 +1,6 @@ -P08100 NP_001009242 96.552 348 12 0 1 348 1 348 0.0 701 +P08100 NP_001009242.1 96.552 348 12 0 1 348 1 348 0.0 701 P08100 0811197A 93.103 348 23 1 1 348 1 347 0.0 673 -P08100 ADB45242 94.817 328 17 0 11 338 1 328 0.0 653 -P08100 ADB45229 94.817 328 17 0 11 338 1 328 0.0 631 -P08100 P56514 84.795 342 51 1 1 341 1 342 0.0 619 -P08100 BAB21486 82.164 342 60 1 1 341 1 342 0.0 599 +P08100 ADB45242.1 94.817 328 17 0 11 338 1 328 0.0 653 +P08100 ADB45229.1 94.817 328 17 0 11 338 1 328 0.0 631 +P08100 P56514.1 84.795 342 51 1 1 341 1 342 0.0 619 +P08100 BAB21486.1 82.164 342 60 1 1 341 1 342 0.0 599 |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastp_four_human_vs_rhodopsin.xml --- a/test-data/blastp_four_human_vs_rhodopsin.xml Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Mon May 28 07:57:56 2018 -0400 |
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| @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastp</BlastOutput_program> - <BlastOutput_version>BLASTP 2.5.0+</BlastOutput_version> + <BlastOutput_version>BLASTP 2.7.1+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Q9BS26</BlastOutput_query-ID> |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastp_four_human_vs_rhodopsin_ext.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Mon May 28 07:57:56 2018 -0400 |
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| b'@@ -1,6 +1,6 @@\n-P08100\tNP_001009242\t96.552\t348\t12\t0\t1\t348\t1\t348\t0.0\t701\tgi|57163783|ref|NP_001009242.1|\t1808\t336\t343\t0\t98.56\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\tMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA\t348\t348\tN/A\n+P08100\tNP_001009242.1\t96.552\t348\t12\t0\t1\t348\t1\t348\t0.0\t701\tgi|57163783|ref|NP_001009242.1|\t1808\t336\t343\t0\t98.56\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\tMNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA\t348\t348\tN/A\n P08100\t0811197A\t93.103\t348\t23\t1\t1\t348\t1\t347\t0.0\t673\tgi|223523|prf||0811197A\t1736\t324\t336\t1\t96.55\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA\tMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA\t348\t347\tN/A\n-P08100\tADB45242\t94.817\t328\t17\t0\t11\t338\t1\t328\t0.0\t653\tgi|283855846|gb|ADB45242.1|\t1684\t311\t321\t0\t97.87\t1\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS\t348\t328\tN/A\n-P08100\tADB45229\t94.817\t328\t17\t0\t11\t338\t1\t328\t0.0\t631\tgi|283855823|gb|ADB45229.1|\t1627\t311\t323\t0\t98.48\t1\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCML'..b'SAATSKTE\t348\t354\tN/A\n-P08100\tBAB21486\t82.164\t342\t60\t1\t1\t341\t1\t342\t0.0\t599\tgi|12583665|dbj|BAB21486.1|\t1544\t281\t314\t1\t91.81\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE\t348\t354\tN/A\n+P08100\tADB45242.1\t94.817\t328\t17\t0\t11\t338\t1\t328\t0.0\t653\tgi|283855846|gb|ADB45242.1|\t1684\t311\t321\t0\t97.87\t1\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS\tVPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS\t348\t328\tN/A\n+P08100\tADB45229.1\t94.817\t328\t17\t0\t11\t338\t1\t328\t0.0\t631\tgi|283855823|gb|ADB45229.1|\t1627\t311\t323\t0\t98.48\t1\t1\tVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS\tVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS\t348\t328\tN/A\n+P08100\tP56514.1\t84.795\t342\t51\t1\t1\t341\t1\t342\t0.0\t619\tgi|3024260|sp|P56514.1|OPSD_BUFBU\t1595\t290\t322\t1\t94.15\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE\tMNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE\t348\t354\tN/A\n+P08100\tBAB21486.1\t82.164\t342\t60\t1\t1\t341\t1\t342\t0.0\t599\tgi|12583665|dbj|BAB21486.1|\t1544\t281\t314\t1\t91.81\t1\t1\tMNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE\tMNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE\t348\t354\tN/A\n' |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/blastx_rhodopsin_vs_four_human.xml --- a/test-data/blastx_rhodopsin_vs_four_human.xml Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Mon May 28 07:57:56 2018 -0400 |
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| @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastx</BlastOutput_program> - <BlastOutput_version>BLASTX 2.5.0+</BlastOutput_version> + <BlastOutput_version>BLASTX 2.7.1+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/cd00003_and_cd00008.pin |
| b |
| Binary file test-data/cd00003_and_cd00008.pin has changed |
| b |
| diff -r d724d9af93ee -r 13aa389f4eeb test-data/four_human_proteins.dbinfo.txt --- a/test-data/four_human_proteins.dbinfo.txt Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/four_human_proteins.dbinfo.txt Mon May 28 07:57:56 2018 -0400 |
| b |
| @@ -1,7 +1,7 @@ Database: Just 4 human proteins 4 sequences; 3,297 total residues -Date: Dec 2, 2016 10:38 AM Longest sequence: 1,382 residues +Date: Oct 31, 2017 4:23 PM Longest sequence: 1,382 residues Volumes: - /mnt/shared/users/pc40583/repositories/galaxy_blast/test-data/four_human_proteins_taxid.fasta + /mnt/galaxy/repositories/galaxy_blast/test-data/four_human_proteins_taxid.fasta |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/four_human_proteins.fasta.pin |
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| Binary file test-data/four_human_proteins.fasta.pin has changed |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/four_human_proteins_taxid.fasta.pin |
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| Binary file test-data/four_human_proteins_taxid.fasta.pin has changed |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/rhodopsin_nucs.dbinfo.txt --- a/test-data/rhodopsin_nucs.dbinfo.txt Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/rhodopsin_nucs.dbinfo.txt Mon May 28 07:57:56 2018 -0400 |
| b |
| @@ -1,7 +1,7 @@ Database: Rhodopsin nucleotides 6 sequences; 10,296 total bases -Date: Dec 2, 2016 10:38 AM Longest sequence: 4,301 bases +Date: Oct 31, 2017 4:23 PM Longest sequence: 4,301 bases Volumes: - /mnt/shared/users/pc40583/repositories/galaxy_blast/test-data/rhodopsin_nucs.fasta + /mnt/galaxy/repositories/galaxy_blast/test-data/rhodopsin_nucs.fasta |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/rhodopsin_nucs.fasta.nin |
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| Binary file test-data/rhodopsin_nucs.fasta.nin has changed |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/tblastn_four_human_vs_rhodopsin.html --- a/test-data/tblastn_four_human_vs_rhodopsin.html Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Mon May 28 07:57:56 2018 -0400 |
| b |
| @@ -1,9 +1,9 @@ <HTML> -<TITLE>BLAST Search Results</TITLE> +<HEAD><TITLE>BLAST Search Results</TITLE></HEAD> <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099"> <PRE> -<b>TBLASTN 2.5.0+</b> +<b>TBLASTN 2.7.1+</b> <b><a |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/tblastn_four_human_vs_rhodopsin.xml --- a/test-data/tblastn_four_human_vs_rhodopsin.xml Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/tblastn_four_human_vs_rhodopsin.xml Mon May 28 07:57:56 2018 -0400 |
| b |
| @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>tblastn</BlastOutput_program> - <BlastOutput_version>TBLASTN 2.5.0+</BlastOutput_version> + <BlastOutput_version>TBLASTN 2.7.1+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular --- a/test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/tblastn_four_human_vs_rhodopsin_deflines.tabular Mon May 28 07:57:56 2018 -0400 |
| b |
| @@ -1,10 +1,10 @@ -P08100 NM_001009242 96.552 348 12 0 1 348 1 1044 0.0 732 -P08100 AB062417 93.391 348 23 0 1 348 1 1044 0.0 711 -P08100 GQ290312 95.092 326 16 0 11 336 1 978 0.0 658 -P08100 U59921 84.795 342 51 1 1 341 42 1067 0.0 646 -P08100 AB043817 82.164 342 60 1 1 341 23 1048 0.0 626 -P08100 GQ290303 93.243 74 5 0 239 312 3147 3368 1.34e-71 151 -P08100 GQ290303 91.525 59 5 0 177 235 2855 3031 1.34e-71 126 -P08100 GQ290303 96.396 111 4 0 11 121 1 333 3.31e-67 229 -P08100 GQ290303 93.220 59 4 0 119 177 1404 1580 2.31e-32 122 -P08100 GQ290303 88.462 26 3 0 312 337 4222 4299 3.61e-12 57.7 +P08100 NM_001009242.1 96.552 348 12 0 1 348 1 1044 0.0 732 +P08100 AB062417.1 93.391 348 23 0 1 348 1 1044 0.0 711 +P08100 GQ290312.1 95.092 326 16 0 11 336 1 978 0.0 658 +P08100 U59921.1 84.795 342 51 1 1 341 42 1067 0.0 646 +P08100 AB043817.1 82.164 342 60 1 1 341 23 1048 0.0 626 +P08100 GQ290303.1 93.243 74 5 0 239 312 3147 3368 1.34e-71 151 +P08100 GQ290303.1 91.525 59 5 0 177 235 2855 3031 1.34e-71 126 +P08100 GQ290303.1 96.396 111 4 0 11 121 1 333 3.31e-67 229 +P08100 GQ290303.1 93.220 59 4 0 119 177 1404 1580 2.31e-32 122 +P08100 GQ290303.1 88.462 26 3 0 312 337 4222 4299 3.61e-12 57.7 |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/three_human_mRNA.dbinfo.txt --- a/test-data/three_human_mRNA.dbinfo.txt Mon Oct 30 11:49:17 2017 -0400 +++ b/test-data/three_human_mRNA.dbinfo.txt Mon May 28 07:57:56 2018 -0400 |
| b |
| @@ -1,7 +1,7 @@ Database: Just 3 human mRNA sequences 3 sequences; 10,732 total bases -Date: Dec 2, 2016 10:38 AM Longest sequence: 4,796 bases +Date: Oct 31, 2017 4:23 PM Longest sequence: 4,796 bases Volumes: - /mnt/shared/users/pc40583/repositories/galaxy_blast/test-data/three_human_mRNA.fasta + /mnt/galaxy/repositories/galaxy_blast/test-data/three_human_mRNA.fasta |
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| diff -r d724d9af93ee -r 13aa389f4eeb test-data/three_human_mRNA.fasta.nin |
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| Binary file test-data/three_human_mRNA.fasta.nin has changed |
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| diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Mon Oct 30 11:49:17 2017 -0400 +++ b/tools/ncbi_blast_plus/README.rst Mon May 28 07:57:56 2018 -0400 |
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| @@ -255,6 +255,10 @@ - Support for ``-window_size``, ``-threshold``, ``-comp_based_stats`` and revising ``-word_size`` to avoid using zero to mean default (contribution from Caleb Easterly). +v0.3.0 - Updated for NCBI BLAST+ 2.7.1, + - Depends on BioConda or legacy ToolShed ``package_blast_plus_2_7_1``. + - Document the BLAST+ 2.6.0 change in the standard 12 column output + from ``qacc,sacc,...`` to ``qaccver,saccver,...`` instead. ======= ====================================================================== |
| b |
| diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Mon Oct 30 11:49:17 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Mon May 28 07:57:56 2018 -0400 |
| b |
| @@ -86,7 +86,7 @@ More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_. .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ -.. _DUST: http://www.ncbi.nlm.nih.gov/pubmed/16796549 +.. _DUST: https://www.ncbi.nlm.nih.gov/pubmed/16796549 **References** |
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| diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Mon Oct 30 11:49:17 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Mon May 28 07:57:56 2018 -0400 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@WRAPPER_VERSION@">0.2.02</token> + <token name="@WRAPPER_VERSION@">0.3.0</token> <xml name="parallelism"> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> @@ -7,7 +7,7 @@ <xml name="preamble"> <requirements> - <requirement type="package" version="2.5.0">blast</requirement> + <requirement type="package" version="2.7.1">blast</requirement> </requirements> <version_command>@BINARY@ -version</version_command> </xml> @@ -288,7 +288,7 @@ <xml name="input_query_gencode"> <param argument="-query_gencode" type="select" label="Query genetic code"> - <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> + <!-- See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> <option value="1" selected="true">1. Standard</option> <option value="2">2. Vertebrate Mitochondrial</option> <option value="3">3. Yeast Mitochondrial</option> @@ -312,7 +312,7 @@ <xml name="input_db_gencode"> <param argument="-db_gencode" type="select" label="Database/subject genetic code"> - <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> + <!-- See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> <option value="1" selected="true">1. Standard</option> <option value="2">2. Vertebrate Mitochondrial</option> <option value="3">3. Yeast Mitochondrial</option> @@ -678,8 +678,8 @@ ====== ========= ============================================ Column NCBI name Description ------ --------- -------------------------------------------- - 1 qacc Query accession - 2 sacc Subject accession (database hit) + 1 qaccver Query accession dot version + 2 saccver Subject accession dot version (database hit) 3 pident Percentage of identical matches 4 length Alignment length 5 mismatch Number of mismatches |
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| diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Oct 30 11:49:17 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon May 28 07:57:56 2018 -0400 |
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| @@ -110,7 +110,7 @@ <param name="hash_index" value="true" /> <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp"> <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" /> - <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" /> + <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" compare="sim_size" delta="0" /> <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" /> <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" /> <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" /> @@ -129,7 +129,7 @@ <param name="taxid" value="9606" /> <output name="outfile" compare="contains" file="four_human_proteins_taxid.fasta.log.txt" ftype="blastdbp"> <extra_files type="file" value="four_human_proteins_taxid.fasta.phr" name="blastdb.phr" /> - <extra_files type="file" value="four_human_proteins_taxid.fasta.pin" name="blastdb.pin" lines_diff="2" /> + <extra_files type="file" value="four_human_proteins_taxid.fasta.pin" name="blastdb.pin" compare="sim_size" delta="0" /> <extra_files type="file" value="four_human_proteins_taxid.fasta.psq" name="blastdb.psq" /> <extra_files type="file" value="four_human_proteins_taxid.fasta.pog" name="blastdb.pog" /> <extra_files type="file" value="four_human_proteins_taxid.fasta.phd" name="blastdb.phd" /> @@ -147,7 +147,7 @@ <param name="mask_data_file" value="segmasker_four_human.maskinfo-asn1" ftype="maskinfo-asn1" /> <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp"> <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" /> - <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" /> + <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" compare="sim_size" delta="0" /> <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" /> <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" /> <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" /> @@ -166,7 +166,7 @@ <param name="taxid" value="9606" /> <output name="outfile" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn"> <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" /> - <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" lines_diff="2" /> + <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" compare="sim_size" delta="8" /> <extra_files type="file" value="three_human_mRNA.fasta.nsq" name="blastdb.nsq" /> <extra_files type="file" value="three_human_mRNA.fasta.nog" name="blastdb.nog" /> <extra_files type="file" value="three_human_mRNA.fasta.nhd" name="blastdb.nhd" /> |
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| diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon Oct 30 11:49:17 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon May 28 07:57:56 2018 -0400 |
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| @@ -75,15 +75,15 @@ (PSSMs) and are available for a number of domain collections including: *CDD* - NCBI curarated meta-collection of domains, see -http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains +https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains *Kog* - PSSMs from automatically aligned sequences and sequence fragments classified in the KOGs resource, the eukaryotic -counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/ +counterpart to COGs, see https://www.ncbi.nlm.nih.gov/COG/ *Cog* - PSSMs from automatically aligned sequences and sequence fragments classified in the COGs resource, which focuses primarily -on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/ +on prokaryotes, see https://www.ncbi.nlm.nih.gov/COG/ *Pfam* - PSSMs from Pfam-A seed alignment database, see http://xfam.org/ @@ -92,11 +92,11 @@ http://smart.embl-heidelberg.de/ *Tigr* - PSSMs from TIGRFAM database of protein families, see -http://www.jcvi.org/cms/research/projects/tigrfams/overview/ +ftp://ftp.jcvi.org/pub/data/TIGRFAMs/ *Prk* - PSSms from automatically aligned stable clusters in the Protein Clusters database, see -http://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters +https://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters The exact list of domain databases offered will depend on how your local Galaxy has been configured. |
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| diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Oct 30 11:49:17 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon May 28 07:57:56 2018 -0400 |
| b |
| @@ -73,15 +73,15 @@ (PSSMs) and are available for a number of domain collections including: *CDD* - NCBI curarated meta-collection of domains, see -http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains +https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains *Kog* - PSSMs from automatically aligned sequences and sequence fragments classified in the KOGs resource, the eukaryotic -counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/ +counterpart to COGs, see https://www.ncbi.nlm.nih.gov/COG/ *Cog* - PSSMs from automatically aligned sequences and sequence fragments classified in the COGs resource, which focuses primarily -on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/ +on prokaryotes, see https://www.ncbi.nlm.nih.gov/COG/ *Pfam* - PSSMs from Pfam-A seed alignment database, see http://xfam.org/ @@ -90,11 +90,11 @@ http://smart.embl-heidelberg.de/ *Tigr* - PSSMs from TIGRFAM database of protein families, see -http://www.jcvi.org/cms/research/projects/tigrfams/overview/ +ftp://ftp.jcvi.org/pub/data/TIGRFAMs/ *Prk* - PSSms from automatically aligned stable clusters in the Protein Clusters database, see -http://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters +https://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters The exact list of domain databases offered will depend on how your local Galaxy has been configured. |
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| diff -r d724d9af93ee -r 13aa389f4eeb tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Mon Oct 30 11:49:17 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Mon May 28 07:57:56 2018 -0400 |
| b |
| @@ -88,7 +88,7 @@ More information about segmasker can be found in the `BLAST Command Line Applications User Manual`_. .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ -.. _SEG: http://www.ncbi.nlm.nih.gov/pubmed/8743706 +.. _SEG: https://www.ncbi.nlm.nih.gov/pubmed/8743706 **References** |