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

[Jason Stajich]

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