representation of binding sites, PSFM and their formal treatment under Information Theory methods are the representation of choice for both deterministic and stochastic methods. Hybrid methods, e.g. ChIPMunk that combines greedy optimization with subsampling, also use PSFM. Recent advances in sequencing have led to the introduction of comparative genomics approaches to DNA binding motif discovery, as exemplified by PhyloGibbs.

More complex methods for binding site search and motif discovery