I've downloaded the scoremats (cdd.tar.gz) from here, and I've been searching for days, but I can't find the answer to my question:
How can I get the matrices that I can get from the PSSM Viewer?
I've tried to get them using some formula someone mentioned in a post here (using h, lambda and kappa), but the numbers didn't match the PSSM viewer.
From what I understand, these files are supposed to serve as a database for RPS-Blast. But looking at examples of how to run RPS-Blast with python, I didn't see the matrix I'm looking for in the output.
So, does anyone have any idea what I need to run to get the actual matrices, or how to convert the files into the PSSMs? it looks like all the data is there, and I just need the right formula. I've read the documentation of the ASN1 format, but that was of no use....