Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon J, Delerce J, Spinelli L, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier L, Hernandez C, Thieffry D, Thomas-Chollier M and van Helden J. RSAT 2015: Regulatory Sequence Analysis Tools. Nucl Acids Res, 43(W1):W50-W56.
RSAT (Regulatory Sequence Analysis Tools) is a suite of modular programs for the analysis
of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery,
appropriate to genome-wide datasets like ChIP-seq, (ii) transcription factor binding motif analysis
(quality assessment, comparisons and clustering), (iii) comparative genomics, (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 reorganised into taxon-specific servers. The suite is well-
documented with tutorials and published protocols. The software suite is available through Web
sites, SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web
services, virtual machines and stand-alone programs at http://www.rsat. eu/.
RSAT (Regulatory Sequence Analysis Tools) is a suite of modular programs for the analysis
of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery,
appropriate to genome-wide datasets like ChIP-seq, (ii) transcription factor binding motif analysis
(quality assessment, comparisons and clustering), (iii) comparative genomics, (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 reorganised into taxon-specific servers. The suite is well-
documented with tutorials and published protocols. The software suite is available through Web
sites, SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web
services, virtual machines and stand-alone programs at http://www.rsat. eu/.