Haktan Suren

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:

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.