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Finding motifs in the twilight zone
1Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA. keich@cs.ucsd.edu
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