MMTSB
Tool Set Documentation

psiblast.pl

From MMTSB
Jump to: navigation, search

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

This script calls BLAST/PSI-BLAST to find sequence alignments for the given sequence. The sequence is read from a file which should contain only the one-letter amino acid sequence either on a single or on multiple lines.

In order for this script to work, BLAST/PSI-BLAST along with recent sequence databases (nr, swissprot, pdbaa) should be installed and the BLAST utilities should be accessible through the search path.

Options

-help 
usage information
-nr 
read sequences from nr (non-redunant complete sequences) database
-pdb 
read sequences from pdbaa (sequences corresponding to PDB structures) database
-db name 
read sequences from other database (needs to be present in BLAST database location)
-eshow value 
E-value threshold for writing out alignments
-ekeep value 
E-value threshold for alignments to be used for profile generation during PSI-BLAST iteration
-n number 
maximum number of alignments to write out
-i number 
number of PSI-BLAST iterations
-gap initial extension 
gap penalties for initiation and extension
-matrix BLOSUM45|BLOSUM50|BLOSUM62|BLOSUM80|PAM250|PAM70|PAM30 
name of sequence scoring matrix
-verbose 
provide extensive output about progress
-log file 
generate log file
-readlog file 
process previously generated log file
-no number 
read alignment with given index and write out in FASTA format

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..