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RSAT: regulatory sequence analysis tools

The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. The suite includes programs for sequence retrieval, pattern discovery, phylogenetic foot...

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Autores principales: Thomas-Chollier, Morgane, Sand, Olivier, Turatsinze, Jean-Valéry, Janky, Rekin's, Defrance, Matthieu, Vervisch, Eric, Brohée, Sylvain, van Helden, Jacques
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447775/
https://www.ncbi.nlm.nih.gov/pubmed/18495751
http://dx.doi.org/10.1093/nar/gkn304
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author Thomas-Chollier, Morgane
Sand, Olivier
Turatsinze, Jean-Valéry
Janky, Rekin's
Defrance, Matthieu
Vervisch, Eric
Brohée, Sylvain
van Helden, Jacques
author_facet Thomas-Chollier, Morgane
Sand, Olivier
Turatsinze, Jean-Valéry
Janky, Rekin's
Defrance, Matthieu
Vervisch, Eric
Brohée, Sylvain
van Helden, Jacques
author_sort Thomas-Chollier, Morgane
collection PubMed
description The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. The suite includes programs for sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and feature map drawing. Random controls can be performed with random gene selections or by generating random sequences according to a variety of background models (Bernoulli, Markov). Beyond the original word-based pattern-discovery tools (oligo-analysis and dyad-analysis), we recently added a battery of tools for matrix-based detection of cis-acting elements, with some original features (adaptive background models, Markov-chain estimation of P-values) that do not exist in other matrix-based scanning tools. The web server offers an intuitive interface, where each program can be accessed either separately or connected to the other tools. In addition, the tools are now available as web services, enabling their integration in programmatic workflows. Genomes are regularly updated from various genome repositories (NCBI and EnsEMBL) and 682 organisms are currently supported. Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published.
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spelling pubmed-24477752008-07-09 RSAT: regulatory sequence analysis tools Thomas-Chollier, Morgane Sand, Olivier Turatsinze, Jean-Valéry Janky, Rekin's Defrance, Matthieu Vervisch, Eric Brohée, Sylvain van Helden, Jacques Nucleic Acids Res Articles The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. The suite includes programs for sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and feature map drawing. Random controls can be performed with random gene selections or by generating random sequences according to a variety of background models (Bernoulli, Markov). Beyond the original word-based pattern-discovery tools (oligo-analysis and dyad-analysis), we recently added a battery of tools for matrix-based detection of cis-acting elements, with some original features (adaptive background models, Markov-chain estimation of P-values) that do not exist in other matrix-based scanning tools. The web server offers an intuitive interface, where each program can be accessed either separately or connected to the other tools. In addition, the tools are now available as web services, enabling their integration in programmatic workflows. Genomes are regularly updated from various genome repositories (NCBI and EnsEMBL) and 682 organisms are currently supported. Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published. Oxford University Press 2008-07-01 2008-05-21 /pmc/articles/PMC2447775/ /pubmed/18495751 http://dx.doi.org/10.1093/nar/gkn304 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Thomas-Chollier, Morgane
Sand, Olivier
Turatsinze, Jean-Valéry
Janky, Rekin's
Defrance, Matthieu
Vervisch, Eric
Brohée, Sylvain
van Helden, Jacques
RSAT: regulatory sequence analysis tools
title RSAT: regulatory sequence analysis tools
title_full RSAT: regulatory sequence analysis tools
title_fullStr RSAT: regulatory sequence analysis tools
title_full_unstemmed RSAT: regulatory sequence analysis tools
title_short RSAT: regulatory sequence analysis tools
title_sort rsat: regulatory sequence analysis tools
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447775/
https://www.ncbi.nlm.nih.gov/pubmed/18495751
http://dx.doi.org/10.1093/nar/gkn304
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