Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Thomas-Chollier, Morgane, Defrance, Matthieu, Medina-Rivera, Alejandra, Sand, Olivier, Herrmann, Carl, Thieffry, Denis, van Helden, Jacques
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
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
_version_ 1782207255919198208
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
work_keys_str_mv AT thomascholliermorgane rsat2011regulatorysequenceanalysistools
AT defrancematthieu rsat2011regulatorysequenceanalysistools
AT medinariveraalejandra rsat2011regulatorysequenceanalysistools
AT sandolivier rsat2011regulatorysequenceanalysistools
AT herrmanncarl rsat2011regulatorysequenceanalysistools
AT thieffrydenis rsat2011regulatorysequenceanalysistools
AT vanheldenjacques rsat2011regulatorysequenceanalysistools