[Bioperl-l] bl2seq

Brian Osborne brian_osborne at cognia.com
Sun Nov 28 12:48:00 EST 2004


You're missing the "database" parameter to the new() call, for you this
would be KS.fasta file. See the bptutorial for an example.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Karolina
Sent: Friday, November 26, 2004 10:57 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] bl2seq

Hi ,

I want to run Bio::Tools::Run::StandAloneBlast (bl2seq) on one sequence
which is
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,


- 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

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