HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites.

Details

Serval ID
serval:BIB_760E10DA7CE2
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites.
Journal
Nucleic Acids Research
Author(s)
Jagannathan V., Roulet E., Delorenzi M., Bucher P.
ISSN
1362-4962[electronic]
Publication state
Published
Issued date
2006
Volume
34
Number
Database issue
Pages
D90-D94
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't - Publication Status: ppublish
Abstract
HTPSELEX is a public database providing access to primary and derived data from high-throughput SELEX experiments aimed at characterizing the binding specificity of transcription factors. The resource is primarily intended to serve computational biologists interested in building models of transcription factor binding sites from large sets of binding sequences. The guiding principle is to make available all information that is relevant for this purpose. For each experiment, we try to provide accurate information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, assembled clone sequences (concatemers) and complete sets of in vitro selected protein-binding tags. In addition, we offer in-house derived binding sites models. HTPSELEX also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols. The FTP site contains the trace archives and database flatfiles. The web server offers user-friendly interfaces for viewing individual entries and quality-controlled download of SELEX sequence libraries according to a user-defined sequencing quality threshold. HTPSELEX is available from ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex/ and http://www.isrec.isb-sib.ch/htpselex.
Keywords
Binding Sites, Computational Biology, DNA/chemistry, DNA/metabolism, Databases, Nucleic Acid, Internet, Regulatory Sequences, Nucleic Acid, SELEX Aptamer Technique, Sequence Analysis, DNA, Transcription Factors/metabolism, User-Computer Interface
Pubmed
Web of science
Open Access
Yes
Create date
13/03/2008 10:32
Last modification date
20/08/2019 14:33
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