RSAT 2015: Regulatory Sequence Analysis Tools

authors

Medina-Rivera Alejandra
Defrance Matthieu
Sand Olivier
Herrmann Carl
Castro-Mondragon Jaime A.
Delerce Jeremy
Jaeger Sébastien
Blanchet Christophe
Vincens Pierre
Caron Christophe
Staines Daniel M.
Contreras-Moreira Bruno
Artufel Marie
Charbonnier-Khamvongsa Lucie
Hernandez Céline
Thieffry Denis
Thomas-Chollier Morgane
Van helden Jacques

document type

ART

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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