NAME
TAIR::Blast - A module to gather automated BLAST result from TAIR (http://www.arabidopsis.org/Blast/index.jsp)
VERSION
Version 1.01
SYNOPSIS
This module simply automatically! BLAST any type of sequences (nucleotide, protein) with using different type of algorithm (blastp, blastn, tblastx etc.) by using TAIR Blast engine.
use TAIR::Blast;
use Bio::DB::Fasta;
my $TB = TAIR::Blast->new();
my $fasta_file = "seqs.fasta";
my $algorithm = "blastn"; #other set : blastp, blastx, tblastx,tblastn
my $maxscore;
my $blast_target_set;
my $verbose = 1;
my $stream = Bio::DB::Fasta->new($fasta_file)->get_PrimarySeq_stream;
while (my $query = $stream->next_seq) {
my $query_seq = $query->seq;
my $result = $TB->connect($query,$query_seq,$algorithm,$maxscore,$blast_target_set,$verbose);
}
my $output_file = "output_file.txt";
$TB->write($output_file);
SUBROUTINES/METHODS
new
Object-oriented master-hash!
connect
Blast parameters, do not mess with them unless you know what you are doing.
write
This subroutine handles output of the program, it writes the blast results into a specified file name.
AUTHOR
Haktan Suren, << <hsuren at cpan.org> >>
BUGS
Please report any bugs or feature requests to bug-tair-blast at rt.cpan.org
, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=TAIR-Blast. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
SUPPORT
You can find documentation for this module with the perldoc command.
perldoc TAIR::Blast
You can also look for information at:
RT: CPAN's request tracker
AnnoCPAN: Annotated CPAN documentation
CPAN Ratings
Search CPAN
DEPENDENCIES
LWP::UserAgent
HTTP::Request::Common
ACKNOWLEDGEMENTS
Special thanks to LC :)
LICENSE AND COPYRIGHT
Copyright 2011 Haktan Suren.
This program is free software; you can redistribute it and/or modify it under the terms of either: the GNU General Public License as published by the Free Software Foundation; or the Artistic License.
See http://dev.perl.org/licenses/ for more information.