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!