[Bioperl-l] Using PSM to find TF site

[Nigam Shah]

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/