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Nucleic Acids Research, 2003, Vol. 31, No. 13 3840-3842
© 2003 Oxford University Press

FootPrinter: a program designed for phylogenetic footprinting

Mathieu Blanchette and Martin Tompa1

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, 1156 High St, Santa Cruz, CA 95064, 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

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of homologous regulatory regions, usually collected from multiple species. It does so by identifying the best conserved motifs in those homologous regions. This note describes web software that has been designed specifically for this purpose, making use of the phylogenetic relationships among the homologous sequences in order to make more accurate predictions. The software is called FootPrinter and is available at http://bio.cs.washington.edu/software.html.


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