[Bioperl-l] Blast against the mouse genome

[pdavid at netvisao.pt]

Your line works for me. This is the script I used:

#/usr/bin/perl -w
use strict;

use Bio::Tools::Run::RemoteBlast;

my $str = Bio::SeqIO->new(-file=>'blast.fa' , '-format' => 'fasta' );
my $prog = 'blastn';
my $db   = 'nr';
my $e_val= '10';

my @params = ( '-prog' => $prog,
	       '-data' => $db,
	       '-expect' => $e_val,
	       '-readmethod' => 'SearchIO' );

my $factory = Bio::Tools::Run::RemoteBlast->new(@params);

#change a paramter
$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Mus
musculus[Organism]';

print STDERR "\n" , $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'}
, "\n";

while (my $input = $str->next_seq()){
    my $r = $factory->submit_blast($input);
    print STDERR "waiting...";
    while ( my @rids = $factory->each_rid ) {
	foreach my $rid ( @rids ) {
	    my $rc = $factory->retrieve_blast($rid);
	    if( !ref($rc) ) {
		if( $rc < 0 ) {
		    $factory->remove_rid($rid);
		}
		print STDERR ".";
		sleep 60;
	    }

	else {
	  my $result = $rc->next_result();
	  #save the output
	  my $filename = $result->query_name();
	  $factory->save_output($filename);
	  $factory->remove_rid($rid);
      }
    }
  }
}


> Hello all,
>
> Apologies for duplication, I found this question in the archives from
> February, but with no reply.
>
> How do I run remote Blast against the mouse genome? I've accomplished
> this with the human genome via a 'chromosome' entry for -data, but this
> only returns human entries. I've changed the parameter like:
>
> $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Mus
> musculus[Organism]';
>
> But to no avail. I've sucessfully checked via the web that my query
> returns mouse genome results. The results page quotes 'contig' as the
> database, but this doesn't work from the script.
>
> Can anyone help?
>
> Cheers,
>
> Jon
>
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