Haktan Suren > TAIR-Blast-1.01 > TAIR::Blast

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Module Version: 1.01   Source  

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.

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