[Bioperl-l] Hit orientation using SearchIO

[Sean ohEigeartaigh]

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.