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

RSAT 2015: Regulatory Sequence Analysis Tools

Alejandra Medina-Rivera  1 , Matthieu Defrance  2 , Olivier Sand  3 , Carl Herrmann  4 , Jaime A Castro-Mondragon  5 , Jeremy Delerce  5 , Sébastien Jaeger  6 , Christophe Blanchet  7 , Pierre Vincens  8 , Christophe Caron  9 , Daniel M Staines  10 , Bruno Contreras-Moreira  11 , Marie Artufel  5 , Lucie Charbonnier-Khamvongsa  5 , Céline Hernandez  8 , Denis Thieffry  8 , Morgane Thomas-Chollier  12 , Jacques van Helden  13
Affiliations

RSAT 2015: Regulatory Sequence Analysis Tools

Alejandra Medina-Rivera et al. Nucleic Acids Res. .

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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Figures

Figure 1.
Figure 1.
Overview of the main applications of RSAT.
See this image and copyright information in PMC

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