[Bioperl-l] 1 small help with WU-BLAST -postsw

Angshu Kar angshu96 at gmail.com
Fri Jan 20 16:34:07 EST 2006


But I'm doing an AND.So if i do use alignment/hit > 0.5 and
alignment/query > 0.5 as a filter will the length of the denominator
matter?

On 1/20/06, Jason Stajich <jason.stajich at duke.edu> wrote:
> Well the hit and query probably are not the same length which is the
> denominator in that fraction ....
>
> On Jan 20, 2006, at 1:57 PM, Angshu Kar wrote:
>
> > Hi,
> >
> > I'm using WU-BLASTP in yeast data (all vs all).
> >
> > Then I'm using :
> >
> > $hit_object->frac_aligned_query() > 0.5
> > and
> > $hit_object->frac_aligned_hit() > 0.5
> >
> > as filter conditions.
> >
> > In that I'm getting asymmetric results! I mean I've sequences A,B in
> > my o/p and not B,A. Has it got something to do with the asymmetry of
> > BLAST (but I thought -postsw takes care of that)?
> >
> > Please help.
> >
> > Thanks,
> > Angshu
> >
> >
> >
> >
> >
> >
> >
> > --
> > Ignore the impossible but honor it ...
> > The only enviable second position is success, since failure always
> > comes first...
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
>
>
>


--
Ignore the impossible but honor it ...
The only enviable second position is success, since failure always
comes first...



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