RSAT 2015: Regulatory Sequence Analysis Tools

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 assessme...

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Published inNucleic acids research Vol. 43; no. W1; pp. W50 - W56
Main 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
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.07.2015
Subjects
Binding Sites
Bioinformatics
Computer Science
Genetic Variation
Genomics
Humans
Internet
Life Sciences
Nucleotide Motifs
Regulatory Elements, Transcriptional
Software
Transcription Factors - metabolism
Web Server issue
Online AccessGet full text
ISSN0305-1048
1362-4962
DOI10.1093/nar/gkv362

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Summary: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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ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkv362