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
Genetics and Genome Biology Program, SickKids Research Institute, Toronto, Canada.
Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
Nucleic Acids Res. 2015 Jul 1;43(W1):W50-6. doi: 10.1093/nar/gkv362. Epub 2015 Apr 22.
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/.
RSAT（调控序列分析工具）是一个用于分析基因组序列中顺式调控元件的模块化软件套件。其主要应用包括：（i）基序发现，适用于ChIP-seq等全基因组数据集；（ii）转录因子结合基序分析（质量评估、比较和聚类）；（iii）比较基因组学；以及（iv）调控变异分析。在2011年《核酸研究》网络软件专刊中描述的43个程序的基础上，又增加了9个新程序，包括一个从坐标列表中提取序列的工具（从UCSC提取序列）、专门用于分析全基因组关联研究（GWAS）或群体基因组学中的调控变异的新程序（检索变异序列和变异扫描）、一个对基序进行聚类并将相似性可视化为树状图的程序（矩阵聚类）。为了应对已测序基因组数量的急剧增加，RSAT公共网站已被重新组织为特定分类单元的服务器。该套件有详细的教程和已发表的协议。该软件套件可通过网站、SOAP/WSDL网络服务、虚拟机以及独立程序在http://www.rsat.eu/获取。
