Question

I am trying to calculate a log-odds matrix for MAST input, froma position-specific probability matrix for the motif in which I aminterested.

I would like to know how MEME estimates the background frequencyof nucleotides, as it does the conversion from position-specificprobability matrices to log-odds matrices when you choose to runMAST on MEME output. Is it simply counting frequencies in thesequences supplied, or is there some sort of modeling going on tocorrect for sample size and whatnot?