TAIR::Blast - A module to gather automated BLAST result from TAIR (http://www.arabidopsis.org/Blast/index.jsp)
Version 1.01
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);
Object-oriented master-hash!
Blast parameters, do not mess with them unless you know what you are doing.
This subroutine handles output of the program, it writes the blast results into a specified file name.
Haktan Suren, << <hsuren at cpan.org> >>
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.
bug-tair-blast at rt.cpan.org
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
http://rt.cpan.org/NoAuth/Bugs.html?Dist=TAIR-Blast
AnnoCPAN: Annotated CPAN documentation
http://annocpan.org/dist/TAIR-Blast
CPAN Ratings
http://cpanratings.perl.org/d/TAIR-Blast
Search CPAN
http://search.cpan.org/dist/TAIR-Blast/
LWP::UserAgent HTTP::Request::Common
Special thanks to LC :)
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.
To install TAIR::Blast, copy and paste the appropriate command in to your terminal.
cpanm
cpanm TAIR::Blast
CPAN shell
perl -MCPAN -e shell install TAIR::Blast
For more information on module installation, please visit the detailed CPAN module installation guide.