[Bioperl-l] Using PSM to find TF site

Jason Stajich jason at cgt.duhs.duke.edu
Thu Jun 24 12:57:46 EDT 2004

TFBS will let you scan.


On Thu, 24 Jun 2004, Nigam Shah wrote:

> Hi!,
> I want to use Bio::Matrix::PSM::SiteMatrixI and a PSM to scan a promoter and
> see if there is a 'hit' for a binding site. From the documentation it seems
> that the way to do it is to get the consensus sequence and then do a regular
> expression match.
> Is there another way of doing it? One that would also give me a
> 'quality-of-hit' score of some kind for the site that was found in the
> promoter?
> Regards,
> Nigam.
> Nigam Shah
> Graduate Fellow,
> Huck Institute for Life Sciences,
> Penn State University.
> Ph:(814)863-5720
> Web: www.personal.psu.edu/nhs109/
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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