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RSAT 2011: regulatory sequence analysis tools
RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated sequence retrieval from EnsEMB...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125777/ https://www.ncbi.nlm.nih.gov/pubmed/21715389 http://dx.doi.org/10.1093/nar/gkr377 |
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author | Thomas-Chollier, Morgane Defrance, Matthieu Medina-Rivera, Alejandra Sand, Olivier Herrmann, Carl Thieffry, Denis van Helden, Jacques |
author_facet | Thomas-Chollier, Morgane Defrance, Matthieu Medina-Rivera, Alejandra Sand, Olivier Herrmann, Carl Thieffry, Denis van Helden, Jacques |
author_sort | Thomas-Chollier, Morgane |
collection | PubMed |
description | RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery algorithms (oligo-diff and info-gibbs), a 100-times faster version of matrix-scan enabling the scanning of genome-scale sequence sets, and a series of facilities for random model generation and statistical evaluation (random-genome-fragments, random-motifs, random-sites, implant-sites, sequence-probability, permute-matrix). Our most recent work also focused on motif comparison (compare-matrices) and evaluation of motif quality (matrix-quality) by combining theoretical and empirical measures to assess the predictive capability of position-specific scoring matrices. To process large collections of peak sequences obtained from ChIP-seq or related technologies, RSAT provides a new program (peak-motifs) that combines several efficient motif discovery algorithms to predict transcription factor binding motifs, match them against motif databases and predict their binding sites. Availability (web site, stand-alone programs and SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services): http://rsat.ulb.ac.be/rsat/. |
format | Online Article Text |
id | pubmed-3125777 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-31257772011-07-05 RSAT 2011: regulatory sequence analysis tools Thomas-Chollier, Morgane Defrance, Matthieu Medina-Rivera, Alejandra Sand, Olivier Herrmann, Carl Thieffry, Denis van Helden, Jacques Nucleic Acids Res Articles RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery algorithms (oligo-diff and info-gibbs), a 100-times faster version of matrix-scan enabling the scanning of genome-scale sequence sets, and a series of facilities for random model generation and statistical evaluation (random-genome-fragments, random-motifs, random-sites, implant-sites, sequence-probability, permute-matrix). Our most recent work also focused on motif comparison (compare-matrices) and evaluation of motif quality (matrix-quality) by combining theoretical and empirical measures to assess the predictive capability of position-specific scoring matrices. To process large collections of peak sequences obtained from ChIP-seq or related technologies, RSAT provides a new program (peak-motifs) that combines several efficient motif discovery algorithms to predict transcription factor binding motifs, match them against motif databases and predict their binding sites. Availability (web site, stand-alone programs and SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services): http://rsat.ulb.ac.be/rsat/. Oxford University Press 2011-07-01 2011-06-27 /pmc/articles/PMC3125777/ /pubmed/21715389 http://dx.doi.org/10.1093/nar/gkr377 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Thomas-Chollier, Morgane Defrance, Matthieu Medina-Rivera, Alejandra Sand, Olivier Herrmann, Carl Thieffry, Denis van Helden, Jacques RSAT 2011: regulatory sequence analysis tools |
title | RSAT 2011: regulatory sequence analysis tools |
title_full | RSAT 2011: regulatory sequence analysis tools |
title_fullStr | RSAT 2011: regulatory sequence analysis tools |
title_full_unstemmed | RSAT 2011: regulatory sequence analysis tools |
title_short | RSAT 2011: regulatory sequence analysis tools |
title_sort | rsat 2011: regulatory sequence analysis tools |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125777/ https://www.ncbi.nlm.nih.gov/pubmed/21715389 http://dx.doi.org/10.1093/nar/gkr377 |
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