psiblast.pl

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]

Show source

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..