CPModule

CPModule is a CRM detection method with a performance that is competitive to that of other state-of-art tools, while being able to handle larger data sets (such as 100 sequences in combination with a library of 517 PWMs).

Resources

Guns, T., Sun, H., Marchal, K., Nijssen, S. (2010) Cis-regulatory module detection using constraint programming. In Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2010) pages:363-368 (IEEE computer society).
Sun, H., Guns, T., Fierro, AC., Thorrez, L., De Moor, B., Nijssen, S., Marchal, K. (2011) Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection. Nucleic Acids Res. 2012 Jul;40(12):e90. doi: 10.1093/nar/gks237.