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Nucleic Acids Research 2006 34(Web Server issue):W578-W583; doi:10.1093/nar/gkl193
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© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

PromAn: an integrated knowledge-based web server dedicated to promoter analysis

Aurélie Lardenois, Frédéric Chalmel1, Laurent Bianchetti2, José-Alain Sahel3, Thierry Léveillard3 and Olivier Poch*

Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/ULP BP 163, 67404 Illkirch Cedex, France 1 Biozentrum and Swiss Institute of Bioinformatics Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland 2 Plate-Forme de Bioinformatique de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/ULP BP 163, 67404 Illkirch Cedex, France 3 Laboratoire de Physiopathologie Cellulaire et Moléculaire de la Rétine, Inserm U592, Université Pierre et Marie Curie 75571 Paris, France

*To whom correspondence should be adressed. Tel: +33 388653294; Fax: +33 388653201; Email: poch{at}igbmc.u-strasbg.fr

Received February 14, 2006. Revised March 21, 2006. Accepted March 21, 2006.

PromAn is a modular web-based tool dedicated to promoter analysis that integrates distinct complementary databases, methods and programs. PromAn provides automatic analysis of a genomic region with minimal prior knowledge of the genomic sequence. Prediction programs and experimental databases are combined to locate the transcription start site (TSS) and the promoter region within a large genomic input sequence. Transcription factor binding sites (TFBSs) can be predicted using several public databases and user-defined motifs. Also, a phylogenetic footprinting strategy, combining multiple alignment of large genomic sequences and assignment of various scores reflecting the evolutionary selection pressure, allows for evaluation and ranking of TFBS predictions. PromAn results can be displayed in an interactive graphical user interface, PromAnGUI. It integrates all of this information to highlight active promoter regions, to identify among the huge number of TFBS predictions those which are the most likely to be potentially functional and to facilitate user refined analysis. Such an integrative approach is essential in the face of a growing number of tools dedicated to promoter analysis in order to propose hypotheses to direct further experimental validations. PromAn is publicly available at http://bips.u-strasbg.fr/PromAn.


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