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Nucleic Acids Research 2006 34(Database Issue):D82-D85; doi:10.1093/nar/gkj146
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Nucleic Acids Research, 2006, Vol. 34, Database issue D82-D85
© The Author 2006. 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}oxfordjournals.org

Article

EPD in its twentieth year: towards complete promoter coverage of selected model organisms

Christoph D. Schmid1, Rouaïda Perier1, Viviane Praz1 and Philipp Bucher1,2,*

1Swiss Institute of Bioinformatics Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland 2Swiss Institute for Experimental Cancer Research Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland

*To whom correspondence should be addressed. Tel: +41 21 6925892 (ext. 58); Fax: +41 21 652 5945; Email: Philipp.Bucher{at}isrec.ch

Received September 17, 2005. Revised October 27, 2005. Accepted October 27, 2005.

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). Access to promoter sequences is provided by pointers to positions in the corresponding genomes. Promoter evidence comes from conventional TSS mapping experiments for individual genes, or, starting from release 73, from mass genome annotation projects. Subsets of promoter sequences with customized 5' and 3' extensions can be downloaded from the EPD website. The focus of current development efforts is to reach complete promoter coverage for important model organisms as soon as possible. To speed up this process, a new class of preliminary promoter entries has been introduced as of release 83, which requires less stringent admission criteria. As part of a continuous integration process, new web-based interfaces have been developed, which allow joint analysis of promoter sequences with other bioinformatics resources developed by our group, in particular programs offered by the Signal Search Analysis Server, and gene expression data stored in the CleanEx database. EPD can be accessed at http://www.epd.isb-sib.ch.


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