[Bioperl-l] BPlite and frames

[Jason Stajich]

On Fri, 10 May 2002, Andy Nunberg wrote:

> Hi,
> I am a new user to bioperl. I am using BPlite to parse blast reports
> (blastn,blastx..) and would
> like to capture frame information for each HSP.  As I iterate over each HSP
> I use the frame subroutine
> but I get a 0-2 number instead of +1 or -3.  Is their a fix to the

These are GFF frames - so +1 is 0 in GFF, -3 will be encoded with a frame
of 2 with the strand being set to -1.

Frames are relative to the hit or query sequence so you need to query it
based on sequence you are interested in.

$hsp->hit->strand()
$hsp->hit->frame()

or
$hsp->query->strand();
$hsp->query->frame();

so the value according to a blast report of -3 can be constructed as

my $blastvalue = ($hsp->query->frame + 1) * $hsp->query->strand;


> subroutine to return the correct values?
> Andy
> *******************************************************************
> Andy Nunberg, Ph.D
> Computational Biologist
> Orion Genomics, LLC
> (314) 615-6989
> http://www.oriongenomics.com
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu