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RSAT 2015: Regulatory sequence analysis tools

AutorMedina-Rivera, Alejandra; Defrance, Matthieu; Sand, Olivier; Herrmann, Carl; Castro-Mondragón, 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
Palabras clavetranscriptional regulation
cis-regulatory elements
cis-regulatory modules (CRMs)
motif discovery
ChIP-seq
regulatory variations
rSNP
comparative genomics
Fecha de publicación2015
EditorOxford University Press
CitaciónMedina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon JA, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier-Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M, van Helden J . RSAT 2015: Regulatory sequence analysis tools. Nucleic Acids Research, Web Server Issue 43 (W1): W50–W56 (2015)
ResumenRSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cisregulatory 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-variationseq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrixclustering). 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/.
Descripción12 Pags.- 1 Tabl.- 1 Fig.
Versión del editorhttp://dx.doi.org/10.1093/nar/gkv362
URIhttp://hdl.handle.net/10261/137226
DOI10.1093/nar/gkv362
ISSN0305-1048
E-ISSN1362-4962
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