[Bioperl-l] Hit orientation using SearchIO

Kevin Brown Kevin.M.Brown at asu.edu
Thu Dec 18 10:09:50 EST 2008

Check the Strand property to determine which orientation the match has.


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Sean ohEigeartaigh
> Sent: Thursday, December 18, 2008 6:00 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Hit orientation using SearchIO
> Hi,
> I'm trying to find out the orientation of blast hits 
> (relative to the query sequence) using SearchIO to process a 
> StandAloneBlast report. I can get the start and end points of 
> the query and the hits using $hsp->start/end('hit'), 
> $hsp->start/end('query') but it always lists the coordinates 
> from lowest to highest. How do I find out if, for example, 
> the query runs 1-60 and the hit runs 240-180? The information 
> is in the BLAST OUT file so it must be accessible.
> Thanks very much for your time,
> Seán Ó hÉigeartaigh, bioinformatics phD student.
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