Difference between TFBS Perl/Biopython motif search and FIMO

Question

[Vishaka Datta]

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.

[Peter]

Given you used MEME, did you consider using its sister tool MAST?

[Vishaka Datta]

FIMO is part of the MEME suite, and it does the job of finding significant matches to a motif. MAST is similar to FIMO in some respects, but does more sophisticated stuff,

I have been trying to replicate results from a paper that used the TFBS Perl module for finding motif matches. They found a much larger number of sequences matching their TFBS motif using TFBS Perl, while I found just (1/3) of the number of matches they got.

The publication wasn't clear on what sort of FDR value adjustment they were doing to get that many matches. Which was why I was unsure if FIMO/MAST work very differently from TFBS Perl.