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Nucleic Acids Research, 2003, Vol. 31, No. 13 3586-3588
© 2003 Oxford University Press

YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation

Saurabh Sinha and Martin Tompa1

Center for Studies in Physics and Biology, Box 25, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA 1 Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195-2350, USA

*To whom correspondence should be addressed. Tel: +1 2065439263; Fax: +1 2065438331; Email: tompa{at}cs.washington.edu

A fundamental challenge facing biologists is to identify DNA binding sites for unknown regulatory factors, given a collection of genes believed to be coregulated. The program YMF identifies good candidates for such binding sites by searching for statistically overrepresented motifs. More specifically, YMF enumerates all motifs in the search space and is guaranteed to produce those motifs with greatest z-scores. This note describes the YMF web software, available at http://bio.cs.washington.edu/software.html.


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