[Bioperl-l] Determining strand orientation from bl2seq report

[Dave Arenillas]

Hi Ewan,

Thanks for the response. Unfortunately I had already tried this (forgot to 
mention in my original post) and for some reason
$hsp->hit->strand always returns 0 regardless of orientation. 
($hsp->query->strand returns 1 as would be expected).

Dave

On Friday 24 January 2003 01:03 am, Ewan Birney wrote:
> On Thu, 23 Jan 2003, Dave Arenillas wrote:
> > I'm trying to figure out if there is any way to determine the strand
> > orientation (Plus / Plus or Plus / Minus) of an HSP from the blast report
> > created by running bl2seq.
> >
> > ex.
> > my @params = ('program' => 'blastn',
> >                 'outfile' => "$BlastFile");
> > my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> > my $report = $factory->bl2seq($seq1, $seq2);
> >
> > while (my $hsp = $report->next_feature) {
> > 	#
> > 	# get orientation info from $hsp???
> > 	#
> > }
> >
> > Apparently Bio::Tools::BPlite::HSP objects have no methods to return this
> > information. I (incorrectly) assumed that I could test
> > $hsp->hit->start > $hsp->hit->end
> > but start is always less than end even for Plus / Minus orientation.
>
> look at $hsp->hit->strand()

-- 
David Arenillas

Bioinformatic Software Developer
Wasserman Lab
Centre for Molecular Medicine and Therapeutics
University of British Columbia
Vancouver, BC Canada
E-mail: dave at cmmt.ubc.ca
Phone: (604) 875-2345 ext. 7948