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

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Serval ID
serval:BIB_31432
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.
Journal
Nucleic Acids Research
Author(s)
Schmid C.D., Praz V., Delorenzi M., Périer R., Bucher P.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
2004
Volume
32
Number
Database issue
Pages
D82-D85
Language
english
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.
Keywords
Animals, Base Sequence, Computational Biology, DNA Primers/genetics, DNA, Complementary/genetics, Databases, Nucleic Acid, Eukaryotic Cells, Expressed Sequence Tags, Humans, Internet, Promoter Regions, Genetic/genetics, Response Elements/genetics, User-Computer Interface
Pubmed
Web of science
Open Access
Yes
Create date
19/11/2007 12:30
Last modification date
25/09/2019 6:08
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