[Bioperl-l] Blast against the mouse genome

[Jonathan Manning]

It all becomes clear... easy once you know how.

Cheers,

Jon

On Fri, 2004-06-04 at 15:00, Jason Stajich wrote:
> 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
>