Tregwiki:Discover motif combinations

• Bayes Promoter scans your sequences for matrix matches and tries to infer a combinations of matrices, with preferred distances and orientation which in turn can be used to scan other sequences.
• a recent paper describes software similar to DPM
• MODULATOR in the cread library (see this wiki, APIs)
• ModuleSearcher
• DASS is a general purpose module finder and claims to be applicable to this problem...