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Bioinformatics Vol. 19 Suppl. 2 2003
pages ii149-ii155
© 2003 Oxford University Press

Finding subtle motifs by branching from sample strings

Alkes Price *, Sriram Ramabhadran and Pavel A. Pevzner

Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093-0114, USA

Received on March 17, 2003 ; accepted on June 9, 2003

Many motif finding algorithms apply local search techniques to a set of seeds. For example, GibbsDNA (Lawrence et al.. 1993, Science , 262, 208–214) applies Gibbs sampling to random seeds, and MEME (Bailey and Elkan, 1994, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology (ISMB-94) , 28–36) applies the EM algorithm to selected sample strings , i.e. substrings of the sample. In the case of subtle motifs, recent benchmarking efforts show that both random seeds and selected sample strings may never get close to the globally optimal motif. We propose a new approach which searches motif space by branching from sample strings, and implement this idea in both pattern-based and profile-based settings. Our PatternBranching and ProfileBranching algorithms achieve favorable results relative to other motif finding algorithms.

Availability: http://www-cse.ucsd.edu/groups/bioinformatics/software.html

Contact: aprice{at}cs.ucsd.edu

* To whom correspondence should be addressed.


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