Dear all,

I need to use the .chk and .pssm files as input for another program. But I am not very sure how to create .chk files and what they actually are. With 'makemat' I can transform .chk to a matrix, but I could not find out what the numbers in the matrix mean.

It seems that, given a sequence fasta, 'blastpgp' performs iterative searches to construct a MSA and create PSSM (.pssm and .chk) as output. But I want to use MSA as input instead.

So how can I obtain these files from a MSA??