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Bioinformatics Advance Access originally published online on March 28, 2008
Bioinformatics 2008 24(10):1307-1309; doi:10.1093/bioinformatics/btn105
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CompariMotif: quick and easy comparisons of sequence motifs

Richard J. Edwards 1,2,*, Norman E. Davey 1 and Denis C. Shields 1

1UCD Complex and Adaptive Systems Laboratory and UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland and 2School of Biological Sciences, University of Southampton, Boldrewood Campus, Southampton SO167PX, UK

*To whom correspondence should be addressed.


  Abstract

Summary: CompariMotif is a novel tool for making motif–motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs.

Availability: CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/

Contact: r.edwards{at}southampton.ac.uk

Supplementary information: Further details are available at http://bioinformatics.ucd.ie/shields/software/comparimotif/

Associate Editor: Burkhard Rost

Received on February 11, 2008; revised on March 18, 2008; accepted on March 19, 2008

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