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Nucleic Acids Res. 2004 Jan 1;32(Database issue):D82-5.

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

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  • 1Swiss Institute of Bioinformatics, Ch. des Boveresses 155, 1066 Epalinges s/Lausanne, Switzerland.

Abstract

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.

PMID:
14681364
[PubMed - indexed for MEDLINE]
PMCID:
PMC308856
Free PMC Article

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