Cargando…

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

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 comp...

Descripción completa

Detalles Bibliográficos
Autores principales: Blanco, Enrique, Farré, Domènec, Albà, M. Mar, Messeguer, Xavier, Guigó, Roderic
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347478/
https://www.ncbi.nlm.nih.gov/pubmed/16381947
http://dx.doi.org/10.1093/nar/gkj116
_version_ 1782126628314284032
author Blanco, Enrique
Farré, Domènec
Albà, M. Mar
Messeguer, Xavier
Guigó, Roderic
author_facet Blanco, Enrique
Farré, Domènec
Albà, M. Mar
Messeguer, Xavier
Guigó, Roderic
author_sort Blanco, Enrique
collection PubMed
description 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 () 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.
format Text
id pubmed-1347478
institution National Center for Biotechnology Information
language English
publishDate 2006
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-13474782006-01-25 ABS: a database of Annotated regulatory Binding Sites from orthologous promoters Blanco, Enrique Farré, Domènec Albà, M. Mar Messeguer, Xavier Guigó, Roderic Nucleic Acids Res Article 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 () 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. Oxford University Press 2006-01-01 2005-12-28 /pmc/articles/PMC1347478/ /pubmed/16381947 http://dx.doi.org/10.1093/nar/gkj116 Text en © The Author 2006. Published by Oxford University Press. All rights reserved
spellingShingle Article
Blanco, Enrique
Farré, Domènec
Albà, M. Mar
Messeguer, Xavier
Guigó, Roderic
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
title ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
title_full ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
title_fullStr ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
title_full_unstemmed ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
title_short ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
title_sort abs: a database of annotated regulatory binding sites from orthologous promoters
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347478/
https://www.ncbi.nlm.nih.gov/pubmed/16381947
http://dx.doi.org/10.1093/nar/gkj116
work_keys_str_mv AT blancoenrique absadatabaseofannotatedregulatorybindingsitesfromorthologouspromoters
AT farredomenec absadatabaseofannotatedregulatorybindingsitesfromorthologouspromoters
AT albammar absadatabaseofannotatedregulatorybindingsitesfromorthologouspromoters
AT messeguerxavier absadatabaseofannotatedregulatorybindingsitesfromorthologouspromoters
AT guigoroderic absadatabaseofannotatedregulatorybindingsitesfromorthologouspromoters