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).
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Tias Guns, Hong Sun, Kathleen Marchal and Siegfried Nijssen
Cis-regulatory Module Detection using Constraint Programming
IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010)