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

Jason Stajich jason.stajich at duke.edu
Fri Jan 20 16:02:22 EST 2006


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...
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12




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