[Bioperl-l] bl2seq

[Karolina Zavisek]

Hi ,

I want to run Bio::Tools::Run::StandAloneBlast (bl2seq) on one sequence which is
standard,
KS, against a list of sequences I got from EMBL retrieved by Bio::DB::EMBL.
Problem is I cannot
make program to read through a list of sequences and to blast2 each of them
against KS sequence.
Any suggestions?

Thank you,

Karolina


- here is a part of program whic executes blast:

#!/usr/bin/perl -w

use strict;
use Bio::Seq;
use Bio::SeqIO;
use Math::BigFloat;
use Bio::SearchIO;
use Bio::Tools::Run::StandAloneBlast;

# input sequence of KS domain
my $query1_in  = Bio::SeqIO->newFh ( -file   => 'KS.fasta',
				                            -format => 'fasta' );
my $query1 = <$query1_in>;


# input a secnd sequence to run a bl2seq program
my $query2_in  = Bio::SeqIO->newFh ( -file   => 'list.fasta',
				    -format => 'fasta' );
my $query2 = <$query2_in>;

while (my $input = $query2->next_seq()) {

# start the bl2seq and save the result in the mybl2seq.bls file
my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => 'blastn',
						                                        'outfile' => 'my_bl2seq.bls');

my $report = $factory->bl2seq($query1, $query2);
}

# and now comes parser



---------------------- T - c o m - - W e b m a i l ----------------------
Ova poruka poslana je upotrebom T-Com Webmail usluge.
http://komunikator.tportal.hr