[ssml] Multiple Alignment to PSSM

[Kevin Karplus]

Dan Bolser wrote

> I remember some tools to convert between HMMER / SAM / PSSM, and I know
> HMMER will make a model from a multiple alignment, so you could then
> convert your HMMER model to a PSSM. Right now I can't find the page of
> these tools. Will psiblast (or related tools in the ncbi toolkit) not do
> it for you?

Probably what Ratna Rajesh Thangudu wanted is best done with
psiblast, but if you want to go through an intermediate stage of
creating an HMM, you are better off using SAM to create the HMM
(though HMMer is probably just as good for scoring the HMM).

Kevin Karplus