[Bioperl-l] Blast against the mouse genome

[Jason Stajich]

You can look at the source for the web cgi page
http://www.ncbi.nlm.nih.gov/genome/seq/MmBlast.html
and deduce the necessary parameters -- that's all we've done.

Presumably you need to set a bunch of the options as listed from the
exerpt of the html form below (there is more so you should look at the
whole thing):
DB_DIR_PREFIX="mm_genome"
DB="genome"
and so forth...

 <form name="listFrm" onSubmit="return CheckThis(this)" method="POST"
action="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi">
	  	<input type="hidden" name="DB_DIR_PREFIX"
value="mouse_contig">
        <input type="hidden" name="DATABASE" value="contig">
        <input type="hidden" name="CMD" value="PUT">
        <input type="hidden" name="AUTO_FORMAT" value="on">
	<input type="hidden" name="WWW_BLAST_TYPE" value="mm_genome">
        <!-- <input type="hidden" name="MEGABLAST" value="on"> -->
<!--table border="0" width="100%" cellspacing="0" cellpadding="0"
bgcolor="#CCCCFF">
          <tr valign="top">
            <td width="304" class="head3">&nbsp;Query Sequence</td>
          </tr>
        </table--> <a href="Database.html">Database</a>:
        <select name="DB" size="1" onChange="HandleDbChange(this.form)">
On
Fri, 4 Jun 2004, Jonathan Manning wrote:

> 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
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> >
> >
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu