[Bioperl-l] Hit orientation using SearchIO
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
> 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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