The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.
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.
Schmid
Christoph D
CD
Swiss Institute of Bioinformatics, Ch. des Boveresses 155, 1066 Epalinges s/Lausanne, Switzerland.
Praz
Viviane
V
Delorenzi
Mauro
M
Périer
Rouaïda
R
Bucher
Philipp
P
D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D017931:DNA Primers / Q000235:genetics*; D018076:DNA, Complementary / Q000235:genetics; D030561:Databases, Nucleic Acid; D005057:Eukaryotic Cells; D020224:Expressed Sequence Tags; D006801:Humans; D020407:Internet; D011401:Promoter Regions, Genetic / Q000235:genetics*; D020218:Response Elements / Q000235:genetics; D014584:User-Computer Interface
D017931:DNA Primers; D018076:DNA, Complementary