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Nucleic Acids Research, 2004, Vol. 32, Database issue D82-D85
© 2004 Oxford University Press

The Eukaryotic Promoter Database EPD: the impact of in silico primer extension

Christoph D. Schmid1, Viviane Praz1,2, Mauro Delorenzi1,2,3, Rouaïda Périer1 and Philipp Bucher*,1,2

1 Swiss Institute of Bioinformatics, 2 Swiss Institute for Experimental Cancer Research and 3 NCCR Molecular Oncology, Ch. des Boveresses 155, 1066 Epalinges s/Lausanne, Switzerland

*To whom correspondence should be addressed. Tel: +41 21 692 5892; Fax: +41 21 652 6933; Email: Philipp.Bucher{at}isrec.unil.ch

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). There may be multiple promoter entries for a single gene. The underlying experimental evidence comes from journal articles and, starting from release 73, from 5' ESTs of full-length cDNA clones used for so-called in silico primer extension. Access to promoter sequences is provided by pointers to TSS positions in nucleotide sequence entries. The annotation part of an EPD entry includes a description of the type and source of the initiation site mapping data, links to other biological databases and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Web-based interfaces have been developed that 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. Tools for analysing sequence motifs around TSSs defined in EPD are provided by the signal search analysis server. EPD can be accessed at http://www.epd. isb-sib.ch.


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