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Bioinformatics Advance Access first published online on November 24, 2006
This version published online on December 5, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl601
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© 2006 The Author(s)
Received September 15, 2006
Revised November 5, 2006
Accepted November 20, 2006

Applications note

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

Tancred Frickey 1 and Georg Weiller 1 *

1 ARC Centre of Excellence for Integrative Legume Research and Bioinformatics Laboratory, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601 Australia

* To whom correspondence should be addressed.
Georg Weiller, E-mail: Georg.Weiller{at}anu.edu.au


  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.

Supplementary_information: http://bioinfoserver.rsbs.anu.edu.au/utils/mclip/info.php.

Associate Editor: John Quackenbush

The corresponding author's email address has been corrected.


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