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Nucleic Acids Research, 2002, Vol. 30, No. 1 322-324
© 2002 Oxford University Press

The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data

Viviane Praz, Rouaïda Périer, Claude Bonnard and Philipp Bucher*

Swiss Institute of Bioinformatics and Swiss Institute for Experimental Cancer Research, Ch. des Boveresses 155, 1066-Epalinges s/Lausanne, Switzerland

The Eukaryotic Promoter Database (EPD) is an annotated, non-redundant collection of eukaryotic Pol II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes a description of the initiation site mapping data, exhaustive cross-references to the EMBL nucleotide sequence database, SWISS-PROT, TRANSFAC and other databases, as well as bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. World Wide Web-based interfaces have been developed which enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria, and to navigate to related databases exploiting different cross-references. The EPD web site also features yearly updated base frequency matrices for major eukaryotic promoter elements. EPD can be accessed at http://www.epd.isb-sib.ch.

* To whom correspondence should be addressed. Tel: +41 21 692 5892; Fax: +41 21 692 5945; Email:philipp.bucher{at}isb-sib.ch


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