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Nucleic Acids Research 2004 32(Web Server Issue):W249-W252; doi:10.1093/nar/gkh372
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

ConSite: web-based prediction of regulatory elements using cross-species comparison

Albin Sandelin, Wyeth W. Wasserman1 and Boris Lenhard*

Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius väg 35, s-17177 Stockholm, Sweden and 1 Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver BC, Canada

* To whom correspondence should be addressed. Tel: +46 8 5248 6391; Fax: +46 8 32 48 26; Email: Boris.Lenhard{at}cgb.ki.se

Received February 16, 2004; Revised and Accepted March 10, 2004

ConSite is a user-friendly, web-based tool for finding cis-regulatory elements in genomic sequences. Predictions are based on the integration of binding site prediction generated with high-quality transcription factor models and cross-species comparison filtering (phylogenetic footprinting). By incorporating evolutionary constraints, selectivity is increased by an order of magnitude as compared to single-sequence analysis. ConSite offers several unique features, including an interactive expert system for retrieving orthologous regulatory sequences. Programming modules and biological databases that form the foundation of the ConSite service are freely available to the research community. ConSite is available at http:/www.phylofoot.org/consite.

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 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.


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