I am trying to calculate a log-odds matrix for MAST input, from a position-specific probability matrix for the motif in which I am interested.
I would like to know how MEME estimates the background frequency of nucleotides, as it does the conversion from position-specific probability matrices to log-odds matrices when you choose to run MAST on MEME output. Is it simply counting frequencies in the sequences supplied, or is there some sort of modeling going on to correct for sample size and whatnot?
EDIT: Another possibility that occurred to me is that MAST is capable of converting position-specific matrices to log-odds matrices. I'd appreciate it if someone could clarify this point for me (and I'm still interested in how the background frequencies are calculated). Also, I am specifically looking for answers with links to supporting documentation.
EDIT 2 (05/07/13): Alexander has answered the original question. Does anyone have an answer to the first edit (re: MAST)?
EDIT 3: MAST doesn't like PSPMs; it will accept the job but crash.