With respect to the FIMO program, I was hoping someone could tell what the preferred input motif format is? I have noticed FIMO runs without error if the motif file format specifies only a log-odds matrix or only a letter-probability matrix. If I use different formats of the same motif (from a MEME output file) then the FIMO results are slightly different. This is using exactly the same background model file as provided to MEME. Does FIMO convert the letter-probability matrix into a log-odds matrix using a different method to the one used in MEME?
Any comments that help give me insight into what is happening "under the hood" and what is best practice would be appreciated.
Cheers,
Richard