[Biopython-dev] Calculating motif scores

[Michiel de Hoon]

> As for the PWM being a separate class and used by the motif:
> I don't know. I'm using Bio.SubsMat.FreqTable for implementing
> frequency table, so I understand that the new PWM class would
> be basically a "smarter" FreqTable. I'm not sure whether it
> solves any problems...

Wow, I didn't even know the Bio.SubsMat module existed. 
As we have several different but related modules (Bio.Motif, Bio.SubstMat, Bio.Align), I think we should define the purpose and scope of each of these modules.
Maybe a good way to start is the documentation. Bio.SubsMat is currently divided into two chapters (14.4 and 16.2). I'll have a look at this over the weekend to see if this can be cleaned up a bit.

--Michiel.