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Nucleic Acids Res. 2015 Jul 1;43(W1):W50-6. doi: 10.1093/nar/gkv362. Epub 2015 Apr 22.

RSAT 2015: Regulatory Sequence Analysis Tools.

Author information

1
Genetics and Genome Biology Program, SickKids Research Institute, Toronto, Canada.
2
Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
3
CNRS-UMR8199 Institut de Biologie de Lille, Génomique Intégrative et Modélisation des Maladies Métaboliques, 1, rue du Pr Calmette, 59000 Lille, France European Genomic Institute for Diabetes (EGID), F-3508, 59000 Lille, France.
4
UMR_S 1090 TAGC, INSERM, Marseille, France; Aix-Marseille Université, Marseille, France Institute of Pharmacy and Molecular Biotechnology, and Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
5
UMR_S 1090 TAGC, INSERM, Marseille, France; Aix-Marseille Université, Marseille, France.
6
Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University, UM2, Marseille, France Institut National de la Santé et de la Recherche Médicale (Inserm), U1104, Marseille, France Centre National de la Recherche Scientifique (CNRS), UMR7280, Marseille, France.
7
CNRS, UMS 3601, Institut Français de Bioinformatique, IFB-core, Avenue de la Terrasse, F-91190 Gif-sur-Yvette, France.
8
Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005, France Inserm, U1024, Paris, F-75005, France CNRS, UMR 8197, Paris, F-75005, France.
9
Station Biologique/Service Informatique et Bio-informatique, Place Georges Teissier - CS 90074, 29688 Roscoff Cedex, France.
10
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
11
Estación Experimental de Aula Dei/CSIC, Av. Montañana 1.005, 50059 Zaragoza, Spain Fundación ARAID, calle María de Luna 11, 50018 Zaragoza, Spain.
12
Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005, France Inserm, U1024, Paris, F-75005, France CNRS, UMR 8197, Paris, F-75005, France mthomas@biologie.ens.fr.
13
European Genomic Institute for Diabetes (EGID), F-3508, 59000 Lille, France Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Campus Plaine, CP 263, Bld du Triomphe, B-1050 Bruxelles, Belgium Jacques.van-Helden@univ-amu.fr.

Abstract

RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/.

PMID:
25904632
PMCID:
PMC4489296
DOI:
10.1093/nar/gkv362
[Indexed for MEDLINE]
Free PMC Article

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