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

  • Authors:

  • Tancred Frickey;Georg Weiller

  • Affiliations:

  • ARC Centre of Excellence for Integrative Legume Research and Bioinformatics Laboratory, Genomic Interactions Group, Research School of Biological Sciences, Australian National University GPO Box ...;ARC Centre of Excellence for Integrative Legume Research and Bioinformatics Laboratory, Genomic Interactions Group, Research School of Biological Sciences, Australian National University GPO Box ...

  • Venue:
  • Bioinformatics
  • Year:
  • 2007

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Abstract

Summary: 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. Availability: The program is available for download from: http://bioinfoserver.rsbs.anu.edu.au/downloads/mclip.jar Contact: Georp.Weiller@anu.edu.au Supplementary information: http://bioinfoserver.rsbs.anu.edu.au/utils/mclip/info.php