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

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dc.contributor.author Blanco, Enrique
dc.contributor.author Farré, Domènec
dc.contributor.author Albà Soler, Mar
dc.contributor.author Messeguer, Xavier
dc.contributor.author Guigó Serra, Roderic
dc.date.accessioned 2011-11-28T11:08:04Z
dc.date.available 2011-11-28T11:08:04Z
dc.date.issued 2006
dc.identifier.citation Blanco E, Farré D, Albà M M, Messeguer X, Guigó R. ABS: a database of annotated regulatory binding sites from orthologous promoters. Nucleic acids research. 2006;34 supl 1:D63-D67. DOI: 10.1093/nar/gkj116
dc.identifier.issn 0305-1048
dc.identifier.uri http://hdl.handle.net/10230/13148
dc.description.abstract 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.
dc.description.sponsorship This work has been supported by grants from Plan/nNacional de I+D (BIO2000-1358-C02-02 and BIO2002-/n04426-C02-01), Ministerio de Ciencia y Tecnología (Spain)/nand from a FBBVA Bioinformatics grant. Funding to pay the/nOpen Access publication charges for this article was provided/nby Ministerio de Ciencia y Tecnología (Spain).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Nucleic Acids Research. 2006;34 supl 1:D63-7
dc.rights © 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.
dc.subject.other Àcids nucleics
dc.subject.other Genòmica -- Bases de dades
dc.subject.other Bioinformàtica
dc.subject.other Interfícies d'usuari (Informàtica)
dc.subject.other Factors de transcripció
dc.title ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/nar/gkj116
dc.subject.keyword Animals
dc.subject.keyword Binding sites
dc.subject.keyword Humans
dc.subject.keyword Mice
dc.subject.keyword Rats
dc.subject.keyword Nucleic Acid
dc.subject.keyword Promoter Regions
dc.subject.keyword User-Computer Interface
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PN/BIO2000-1358
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PN/BIO2002-4426
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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