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

[Hilmar Lapp]

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
> 
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