Mclip: motif detection based on cliques of gapped local profile-to-profile alignments

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A multitude of motif-finding tools have been published, which can generally be assigned to one of three classes: expectation-maximization, Gibbs-sampling or enumeration. Irrespective of this grouping, most motif detection tools only take into account similarities across ungapped sequence regions, possibly causing short motifs located peripherally and in varying distance to a ‘core’ motif to be missed. We present a new method, adding to the set of expectation-maximization approaches, that permits the use of gapped alignments for motif elucidation.

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