I've learnt a motif file for a TF from running meme on a ChIP-seq data set.
I now want to search for matches to this motif in the remainder of my ChIP-seq data set. One option is to use FIMO with the motif file to search for motif occurrences, and the other is to use the biopython motif search package using position frequency matrices.
I like FIMO currently because of the control offered on threshold p and q-values. Does anyone know how the FIMO search method differs from that implemented in biopython or TFBS Perl? Are the underlying algorithms similar? I can't seem to find much documentation on this.