RSAT 2015: Regulatory Sequence Analysis Tools

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2015 Apr 24

PMID 25904632

Citations 145

Authors

Alejandra Medina-Rivera

Matthieu Defrance

Olivier Sand

Carl Herrmann

Jaime A Castro-Mondragon

Jeremy Delerce

Sebastien Jaeger

Christophe Blanchet

Pierre Vincens

Christophe Caron

Daniel M Staines

Bruno Contreras-Moreira

Marie Artufel

Lucie Charbonnier-Khamvongsa

Celine Hernandez

Denis Thieffry

Morgane Thomas-Chollier

Jacques van Helden

Affiliations

Soon will be listed here.

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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