I have a number of PWMs (8 positions) for several TFs I'd like to scan a genome with, and I've been suggested to use the FIMO tool from the MEME suit for this (http://meme.sdsc.edu/meme/cgi-bin/fimo.cgi)
This, however, requires a background model for the organism. A friend mentioned that the accepted way to do this is to simply use a 4th Order Markov Model using the whole genome.
So, what I'd like to ask you is:
(1) Would you agree with the use of FIMO for my problem of scanning and finding statistically significant potential targets of my TFs of interest? If not, what other platforms would you recommend? RSAT? Other?
(2) Do you think that the Markov model approach is the best one for getting a background model? Can background models be included in other methods for identifying potential targets through the use of PWMs?
Thanks in advance!