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Nucleic Acids Research 2006 34(Database Issue):D63-D67; doi:10.1093/nar/gkj116
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Nucleic Acids Research, 2006, Vol. 34, Database issue D63-D67
© 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

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters

Enrique Blanco1,2,*, Domènec Farré1,2, M. Mar Albà1, Xavier Messeguer2 and Roderic Guigó1

1Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica/Universitat Pompeu Fabra/Centre de Regulació Genòmica C/Doctor Aiguader 80, 08003 Barcelona, Spain 2Grup d'algorísmica i genètica, Departament de Llenguatges i Sistemes Informàtics, Universitat Politècnica de Catalunya C/Jordi Girona 1–3, 08034 Barcelona, Spain

*To whom correspondence should be addressed. Tel: +34 93 2240891; Fax: +34 93 2240875; Email: eblanco{at}imim.es

Received August 1, 2005. Revised September 19, 2005. Accepted October 18, 2005.

Information about the genomic coordinates and the sequence of experimentally identified transcription factor binding sites is found scattered under a variety of diverse formats. The availability of standard collections of such high-quality data is important to design, evaluate and improve novel computational approaches to identify binding motifs on promoter sequences from related genes. ABS (http://genome.imim.es/datasets/abs2005/index.html) is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. A simple and easy-to-use web interface facilitates data retrieval allowing different views of the information. In addition, the release 1.0 of ABS includes a customizable generator of artificial datasets based on the known sites contained in the collection and an evaluation tool to aid during the training and the assessment of motif-finding programs.


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