Dissemin is shutting down on January 1st, 2025

Published in

Oxford University Press, Nucleic Acids Research, W1(43), p. W50-W56, 2015

DOI: 10.1093/nar/gkv362

Oxford University Press, Nucleic Acids Research, suppl(39), p. W86-W91, 2011

DOI: 10.1093/nar/gkr377

Oxford University Press, Nucleic Acids Research, Web Server(36), p. W119-W127, 2008

DOI: 10.1093/nar/gkn304

Links

Tools

Export citation

Search in Google Scholar

RSAT 2015: Regulatory Sequence Analysis Tools

Journal article published in 2015 by Alejandra Medina-Rivera, Jaime A. Castro-Mondragon, J.-V. Turatsinze, Matthieu Defrance, Jeremy Delerce, Olivier Sand, Sébastien Jaeger, Carl Herrmann, Christophe Blanchet, R. Janky, Pierre Vincens, Morgane Thomas-Chollier, Christophe Caron, Daniel M. Staines, Bruno Contreras-Moreira and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

Full text: Download

Green circle
Preprint: archiving allowed
Upload
Green circle
Postprint: archiving allowed
Upload
Green circle
Published version: archiving allowed
Upload
Policy details
Data provided by SHERPA/RoMEO

Abstract

The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. The suite includes programs for sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and feature map drawing. Random controls can be performed with random gene selections or by generating random sequences according to a variety of background models (Bernoulli, Markov). Beyond the original word-based pattern-discovery tools (oligo-analysis and dyad-analysis), we recently added a battery of tools for matrix-based detection of cis-acting elements, with some original features (adaptive background models, Markov-chain estimation of P-values) that do not exist in other matrix-based scanning tools. The web server offers an intuitive interface, where each program can be accessed either separately or connected to the other tools. In addition, the tools are now available as web services, enabling their integration in programmatic workflows. Genomes are regularly updated from various genome repositories (NCBI and EnsEMBL) and 682 organisms are currently supported. Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published. ; Journal Article ; Research Support, Non-U.S. Gov't ; SCOPUS: ar.j ; info:eu-repo/semantics/published