|
|
Difference between revisions of "Psiblast.pl"
From MMTSB
| Line 6: | Line 6: | ||
== Description == | == 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.<BR> | ||
| + | |||
| + | 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.<BR> | ||
== Options == | == Options == | ||
; -help : usage information | ; -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 == | ||
| + | <mmtsbToolExample cmd="psiblast.pl" set="test1"></mmtsbToolExample> | ||
| − | == | + | <mmtsbToolExample cmd="psiblast.pl" set="test2"></mmtsbToolExample> |
Latest revision as of 22:55, 13 September 2010
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
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..