RSAT 2011: regulatory sequence analysis tools

Morgane Thomas-Chollier (1) , Olivier Sand (1) , Jean-Valery Turatsinze (1) , Rekin'S Janky (1) , Matthieu Defrance (1) , Eric Vervisch (1) , Sylvain Brohee (1) , Jacques Van Helden (1)

1 BiGRe - Laboratoire de Bioinformatique des Génomes et des Réseaux

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.

Domains: Computer Science [cs]; Bioinformatics [q-bio.QM]; Life Sciences [q-bio]

Morgane Thomas-Chollier, Olivier Sand, Jean-Valery Turatsinze, Rekin'S Janky, Matthieu Defrance, et al.. RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Research, 2011, 39, pp.W86--W91. ⟨10.1093/nar/gkr377⟩. ⟨hal-01624291⟩