title: RSAT 2015: Regulatory Sequence Analysis Tools.
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/.
authors.affiliation: Genetics and Genome Biology Program, SickKids Research Institute, Toronto, Canada.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Medina-Rivera
authors.affiliation: Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Defrance
authors.affiliation: 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.
authors.forename: Olivier
authors.initials: O
authors.lastname: Sand
authors.affiliation: 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.
authors.forename: Carl
authors.initials: C
authors.lastname: Herrmann
authors.affiliation: UMR_S 1090 TAGC, INSERM, Marseille, France; Aix-Marseille Université, Marseille, France.
authors.forename: Jaime A
authors.initials: JA
authors.lastname: Castro-Mondragon
authors.affiliation: UMR_S 1090 TAGC, INSERM, Marseille, France; Aix-Marseille Université, Marseille, France.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Delerce
authors.affiliation: 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.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Jaeger
authors.affiliation: CNRS, UMS 3601, Institut Français de Bioinformatique, IFB-core, Avenue de la Terrasse, F-91190 Gif-sur-Yvette, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Blanchet
authors.affiliation: 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.
authors.forename: Pierre
authors.initials: P
authors.lastname: Vincens
authors.affiliation: Station Biologique/Service Informatique et Bio-informatique, Place Georges Teissier - CS 90074, 29688 Roscoff Cedex, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Caron
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Staines
authors.affiliation: Estación Experimental de Aula Dei/CSIC, Av. Montañana 1.005, 50059 Zaragoza, Spain Fundación ARAID, calle María de Luna 11, 50018 Zaragoza, Spain.
authors.forename: Bruno
authors.initials: B
authors.lastname: Contreras-Moreira
authors.affiliation: UMR_S 1090 TAGC, INSERM, Marseille, France; Aix-Marseille Université, Marseille, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Artufel
authors.affiliation: UMR_S 1090 TAGC, INSERM, Marseille, France; Aix-Marseille Université, Marseille, France.
authors.forename: Lucie
authors.initials: L
authors.lastname: Charbonnier-Khamvongsa
authors.affiliation: 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.
authors.forename: Céline
authors.initials: C
authors.lastname: Hernandez
authors.affiliation: 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.
authors.forename: Denis
authors.initials: D
authors.lastname: Thieffry
authors.affiliation: 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.
authors.forename: Morgane
authors.initials: M
authors.lastname: Thomas-Chollier
authors.affiliation: 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.
authors.forename: Jacques
authors.initials: J
authors.lastname: van Helden
mesh_terms: D001665:Binding Sites; D014644:Genetic Variation; D023281:Genomics; D006801:Humans; D020407:Internet; D059372:Nucleotide Motifs; D050436:Regulatory Elements, Transcriptional; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors