Get FIMO PSSM from position probability matrix

[Bharata Kalbuaji]

So, I have downloaded position frequency matrix from transfac which then I use transfac2meme to get position probability matrix. From reading this group, it seems FIMO convert the matrix inputted into a PSSM given the background file. So, is there any method to convert position probability matrix into PSSM via command line? I read the source code and there is a function build_motif_pssm in the pssm.c file. Thank you.

[CharlesEGrant]

You can direct transfac2meme to generate the PSSM using the -logodds option. This is described in the help page for transfac2meme. Note though that raw scores from the PSSM are generally less useful then p-value or q-values. The problem being that you can't directly compare raw score for matches to different motifs.