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ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
Blanco, Enrique; Farré, Domènec; Albà Soler, Mar; Messeguer, Xavier; Guigó Serra, Roderic
Universitat Pompeu Fabra
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.
This work has been supported by grants from PlanNacional de I+D (BIO2000-1358-C02-02 and BIO2002-04426-C02-01), Ministerio de Ciencia y Tecnología (Spain)and from a FBBVA Bioinformatics grant. Funding to pay theOpen Access publication charges for this article was providedby Ministerio de Ciencia y Tecnología (Spain).
02-07-2013
Genòmica -- Bases de dades
Àcids nucleics
Bioinformàtica
Interfícies d'usuari (Informàtica)
Factors de transcripció
Animals
Binding sites
Humans
Mice
Rats
Nucleic Acid
Promoter Regions
User-Computer Interface
© The Authors 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. Published article is also available at http://nar.oxfordjournals.org/content/34/suppl_1/D63.
Artículo
info:eu-repo/semantics/publishedVersion
Oxford University Press
         

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