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Finding motifs in the twilight zone

2002; Oxford University Press; Volume: 18; Issue: 10 Linguagem: Inglês

10.1093/bioinformatics/18.10.1374

1367-4811

Uri Keich, Pavel A. Pevzner,

Ancient and Medieval Archaeology Studies

Abstract 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@cs.ucsd.edu * To whom correspondence should be addressed.