Hi folks,
I'm looking for a tool that will allow me to input a list of transcription factor pwms to search against a set of query and control sequences (ex: enhancers of type A and B), reporting enrichment. The goal here is to get an idea of what a typical member of the query sequence looks like - what tfbs are over- and under-represented. My first thought was to use AME of the MEME suite, but it only expresses enrichment in terms of p values. Is there something else out there that is better suited to my goals?
Alternatively - I'm familiar with how to get a count of motifs for each tfbs and can image normalizing with respect to sequence length to determine relative tfbs frequency between the sequence sets. Are there other parameters that I should keep in mind when calculating fold enrichment?
Thanks for your time!
Homer could be useful. It does searching for known TF motifs as well as search for novel enriched motifs. http://homer.salk.edu/homer/motif/