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Difference between revisions of "psiblast.pl"
From MMTSB
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== Examples == | == Examples == | ||
− | <mmtsbToolExample cmd=" | + | |
+ | <mmtsbToolExample cmd="psiblast.pl" set="test1"></mmtsbToolExample> | ||
+ | |||
+ | <mmtsbToolExample cmd="psiblast.pl" set="test2"></mmtsbToolExample> |
Revision as of 15:23, 30 July 2009
Usage
usage: psiblast.pl [options] [seqFile] options: [-nr] [-pdb] [-db name] [-eshow value] [-ekeep value] [-n alignments] [-i iterations] [-gap initial extension] [-matrix BLOSUM45|BLOSUM50|BLOSUM62|BLOSUM80|PAM250|PAM70|PAM30] [-verbose] [-log file] [-readlog file] [-no value] [-csblast]
Description
Options
- -help
- usage information
Examples
psiblast.pl -pdb -log psiblast.log sequence
align the given sequence to sequences from the PDB and generate a log file with the output from PSI-BLAST
>TARGET RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELIP >1IHG_A ::4e-96::61::Chain A, Bovine Cyclophilin 40, Monoclinic Form NPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEVK-GEKPAKLCVIAECGEL.. >TARGET RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELIP >2RMA_A ::4e-96::52::Chain A, Crystal Structures Of Cyclophilin A Complexed With NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG--------YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGS-RNGKTSKKITIADCGQL.. >TARGET RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELIP ...
psiblast.pl -pdb -readlog psiblast.log -no 4 sequence
extract alignment number 4 from the log file of a previous PSI-BLAST run
>TARGET RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELIP >5CYH_A ::5e-96::52::Chain A, Cyclophilin A Complexed With Dipeptide Gly-Pro NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG--------YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGS-RNGKTSKKITIADCGQL..