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EPD


NAR Molecular Biology Database Collection entry number 33
Cavin PÉrier, R.1, Praz, V.2, Bucher, P.2
1Swiss Institute of Bioinformatics Ch. des Boveresses 155 1066 Epalinges, Switzerland
2Swiss Institute for Experimental Cancer Reaserch Ch. des Boveresses 155 1066 Epalinges, Switzerland

Database Description

The Eukaryotic Promoter Database 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 description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. WWW-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extrac 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.

Recent Developments

New links to gene expression date are provided by the companion database EPDEX. We started to add new EPD entries based on full length cDNA sequences from the NEDO and MGC projects. These entries are generated in a semi-automatic fashion.

Acknowledgements

EPD is funded by grants from the Swiss federal government.

References

Praz, V., PÉrier, R., Bonnard, C., Bucher, P. (2002). The Eukaryotic Promoter Database EPD: New entry types and links gene expression data. Nucleic Acids Res. 30, 322-324


Go to the abstract in the NAR 2006 Database Issue.
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