[Bioperl-l] blasting with multiple query sequences?

[Jason Stajich]

Also

$hsp->query->seqname

On Fri, 4 Oct 2002, Jason Stajich wrote:

>
> $report->query_name
> $report->query_description
>
> On Fri, 4 Oct 2002, Tobias Thierer wrote:
>
> > Hi,
> >
> > Bio::Tools::Run::StandAloneBlast::blastall
> >
> > accepts a reference to an array of Bio::Seq objects.
> > If such a reference is passed, all the sequences in
> > the array will be blasted against the specified database.
> >
> > However, although I verbosely browsed the documentation,
> > I could not find any hint on how to get the sequence
> > that belongs to a specific Subject or HSP. The BLAST
> > report gives me all HSPs grouped by subject, but it
> > seems that I have no way to actually find out which of
> > the sequences that I passed to blastall() actually caused
> > the hit.
> >
> > I'd really appreciate if someone could tell me if and
> > how this is possible. I need to blast multiple sequences
> > against a database, and get the high scoring matches for
> > each query sequence. The blast report, however, groups
> > the blast result by subject, where each subject consists
> > of a number of HSPs. $hsp->query is only a
> > Bio::SeqFeature::Similarity object, not the original
> > sequence object. If I pass only one sequence to
> > blastall() at a time, the blast executable will be run
> > multiple times and thus the database will innecessarily
> > be loaded multiple times from the hard disk into the
> > memory.
> >
> > Any help would really be appreciated!
> >
> > Regards,
> >
> >   Tobias
> >
> >
> > P.S.: Here is what I am currently doing:
> >
> >   # ($sequences is a reference to an array of Bio::Seq
> >   # objects)
> >
> >   my $report = $blaster->blastall($sequences);
> >   while(my $sbjct = $report->nextSbjct) {
> >     while (my $hsp = $sbjct->nextHSP) {
> >
> >       # How can I find out which of the sequences in
> >       # @$sequences caused the hit?
> >
> >       print "some sequence matched at ", $hsp->query->start,"->",
> > 	 $hsp->query->end, "\n";
> >     }
> >   }
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu