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Bioinformatics Vol. 18 no. 10 2002
Pages 1374-1381
© 2002 Oxford University Press

Finding motifs in the twilight zone

U. Keich 1,* and P.A. Pevzner 1

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

Received on February 1, 2002 ; revised on March 25, 2002 ; accepted on April 5, 2002

Motivation: Gene activity is often affected by binding transcription factors to short fragments in DNA sequences called motifs. Identification of subtle regulatory motifs in a DNA sequence is a difficult pattern recognition problem. In this paper we design a new motif finding algorithm that can detect very subtle motifs.

Results: We introduce the notion of a multiprofile and use it for finding subtle motifs in DNA sequences. Multiprofiles generalize the notion of a profile and allow one to detect subtle patterns that escape detection by the standard profiles. Our MULTIPROFILER algorithm outperforms other leading motif finding algorithms in a number of synthetic models. Moreover, it can be shown that in some previously studied motif models, MULTIPROFILER is capable of pushing the performance envelope to its theoretical limits.

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

Contact: keich{at}cs.ucsd.edu

* To whom correspondence should be addressed.


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