[Bioperl-l] Blast against the mouse genome

[Jonathan Manning]

Thanks for the reply. Yep, you're right, it works fine Blasting against
the non-redundant database. But how do I do a genome search? nr does not
return genome matches for a query which I have successfully performed
via the mouse genome page online.



On Fri, 2004-06-04 at 14:25, pdavid at netvisao.pt wrote:
> 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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> >
> 
>