[Bioperl-l] orientation of HSPs

[Jason Stajich]

I believe that $hsp->subject->strand will help you.  Let us know if it
does not report what you expect.

Would the GD::Graph + BPlite ploting script possibly available for public
consumption at some point? 

-jason
On Tue, 31 Jul 2001, Gregory Carl Kettler wrote:

> I've been using the BPlite parser along with GD::Graph to plot the
> locations of BLAST hits on very long DNA sequences, and recently thought I
> might want to know the orientations of these hits.  
> If there is a hit to the reverse compliment of the database
> sequence (i.e. the opposite strand), this is reflected in the BLAST output
> by an alignment diagram that shows sbjct start > sbjct end.  
> I had hoped this would be reflected by the truth of the Perl code:
> $hsp->subject->start > $hsp->subject->end
> but that seems not to be the case.  It looks like it's always rearranged 
> so start < end.  Is there a better way to get the information I need?  If
> not, where do I go in the source code to prevent that rearrangement?
> 
> 		Greg Kettler
> 	Student of Biology and Computer Science
> 		University of Chicago
> "Of course, if you're writing the code to control a cruise missile, you
> may not actually need an explicit loop exit.  The loop will be terminated
> automatically at the appropriate moment."    --Programming Perl, 3rd Ed.
> 
> 
> 
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/