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RSAT 2015: Regulatory Sequence Analysis Tools.

Authors
  • Medina-Rivera A,1
  • Defrance M,2
  • Sand O,3
  • Herrmann C,4
  • Castro-Mondragon JA,5
  • Delerce J,5
  • Jaeger S,6
  • Blanchet C,7
  • Vincens P,8
  • Caron C,9
  • Staines DM,10
  • Contreras-Moreira B,11
  • Artufel M,5
  • Charbonnier-Khamvongsa L,5
  • Celine Hernandez8
  • Thieffry D,8
  • Thomas-Chollier M,12
  • van Helden J,13
Type
Published Article
Journal
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Publication Date
Jul 16, 2015
Volume
43
Issue
W1
Identifiers
DOI: 10.1093/nar/gkv362
Source
MyScienceWork
License
Green

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/.

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