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Nucleic Acids Research 2006 34(Database Issue):D90-D94; doi:10.1093/nar/gkj049
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Nucleic Acids Research, 2006, Vol. 34, Database issue D90-D94
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

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

Vidhya Jagannathan, Emmanuelle Roulet, Mauro Delorenzi and Philipp Bucher*

Swiss Institute for Experimental Cancer Research and Swiss Institute of Bioinformatics Ch. des Boveresses 155, CH-1066 Epalinges, Switzerland

*To whom correspondence should be addressed. Tel: +41 21 692 5892/58; Fax: +41 21 652 5945; Email: Philipp.Bucher{at}isrec.ch

Received August 15, 2005. Revised October 4, 2005. Accepted October 4, 2005.

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.


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