[Bioperl-l] Start and end of query sequence in HSPs

[Jason Stajich]

You can also search them:

http://users.bioperl.org/htdig/

On Wed, 16 Oct 2002, Hilmar Lapp wrote:

> I'm not sure whether everyone is comfortable wading through or
> searching through email archives (I can only encourage those who are
> timid -- you find stuff nicely most of the time). However, there's a
> nicely written HOWTO for the SearchIO modules as well (written by ...
> Jason! :) - this should be a must read if you want to take full
> advantage of those modules.
>
> 	-hilmar
>
> > -----Original Message-----
> > From: Jason Stajich [mailto:jason@cgt.mc.duke.edu]
> > Sent: Wednesday, October 16, 2002 8:21 AM
> > To: Kasper Munch Terkelsen
> > Cc: bioperl-l@bioperl.org
> > Subject: Re: [Bioperl-l] Start and end of query sequence in HSPs
> >
> >
> > Please consider reading the mailing list archives, this has
> > been answered
> > multiple times.
> >
> > $hsp->subject->start
> > $hsp->subject->end
> >
> >
> > On Wed, 16 Oct 2002, Kasper Munch Terkelsen wrote:
> >
> > > Dear all
> > >
> > > Does anyone know how to get hold of the start and end positions of a
> > > sbjct sequence in a HSP? I am using the StandAloneBlast module, so I
> > > think I am confined to using the Search and SearchIO
> > modules to parse
> > > the BLAST reports because the blastall method returns a blast
> > > object. So what I am after is simply the two numbers at the ends of
> > > each HSP as they appear in the blast report. Please help me, I am
> > > desperate!
> > >
> > > Regards Kasper
> > >
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
> > _______________________________________________
> > 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