Which tool for CRM enrichment?

Question

[Filago]

Hello guys,

I am interested in conducting CRM (cis-regulatory module) enrichment analysis in selected sequences. Screening the literature, I figured out, that a lot of tools in that field were published in the early 2000s and are not available anymore (rly. frustrating to click on all that "links to nowhere" :) ). On the other hand, the still available tools tend to be Web-server solutions, what makes custom preferences more complicated/impossible.

Maybe someone knows a CRM enrichment tool fulfilling the following points:

1. Local installation (so no web-server)
2. Custom sequences and custom TFBS allowed
3. Capability to deal with a large number of TFBS

Many thanks in advance!

Andreas

[ATpoint]

What is "CRM enrichment analysis"?

[Filago]

Hello, a CRM enrichment analysis is an enrichment analysis of TFBS-pairs (but can also be TFBS-trios, TFBS-quartets...) in e.g. promoters of a certain gene set compared to a background geneset.

Best, Andreas