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Nucleic Acids Research 2005 33(Web Server Issue):W442-W446; doi:10.1093/nar/gki420
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting

David L. Corcoran1,2, Eleanor Feingold1,2 and Panayiotis V. Benos1,3,4,*

1Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh Pittsburgh, PA, USA 2Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh Pittsburgh, PA, USA 3Department of Computational Biology, University of Pittsburgh Pittsburgh, PA, USA 4University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh Pittsburgh, PA, USA

*To whom correspondence should be addressed. Tel: +1 412 648 3315; Fax: +1 412 624 3020; Email: benos{at}pitt.edu

Received February 14, 2005. Revised March 21, 2005. Accepted March 21, 2005.

FOOTER is a newly developed algorithm that analyzes homologous mammalian promoter sequences in order to identify transcriptional DNA regulatory ‘signals’. FOOTER uses prior knowledge about the binding site preferences of the transcription factors (TFs) in the form of position-specific scoring matrices (PSSMs). The PSSM models are generated from known mammalian binding sites from the TRANSFAC database. In a test set of 72 confirmed binding sites (most of them not present in TRANSFAC) of 19 TFs, it exhibited 83% sensitivity and 72% specificity. FOOTER is accessible over the web at http://biodev.hgen.pitt.edu/Footer/.


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