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Nucleic Acids Research 2005 33(Web Server Issue):W447-W450; doi:10.1093/nar/gki378
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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

CONREAL web server: identification and visualization of conserved transcription factor binding sites

Eugene Berezikov*, Victor Guryev and Edwin Cuppen

Hubrecht Laboratory Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands

*To whom correspondence should be addressed. Tel: +30 2121828; Fax: +30 2516464; Email: berezikov{at}niob.knaw.nl

Received February 14, 2005. Revised March 8, 2005. Accepted March 8, 2005.

The use of orthologous sequences and phylogenetic footprinting approaches have become popular for the recognition of conserved and potentially functional sequences. Several algorithms have been developed for the identification of conserved transcription factor binding sites (TFBSs), which are characterized by their relatively short and degenerative recognition sequences. The CONREAL (conserved regulatory elements anchored alignment) web server provides a versatile interface to CONREAL-, LAGAN-, BLASTZ- and AVID-based predictions of conserved TFBSs in orthologous promoters. Comparative analysis using different algorithms can be started by keyword without any prior sequence retrieval. The interface is available at http://conreal.niob.knaw.nl.


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