title: RSAT 2011: regulatory sequence analysis tools.
abstract: RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery algorithms (oligo-diff and info-gibbs), a 100-times faster version of matrix-scan enabling the scanning of genome-scale sequence sets, and a series of facilities for random model generation and statistical evaluation (random-genome-fragments, random-motifs, random-sites, implant-sites, sequence-probability, permute-matrix). Our most recent work also focused on motif comparison (compare-matrices) and evaluation of motif quality (matrix-quality) by combining theoretical and empirical measures to assess the predictive capability of position-specific scoring matrices. To process large collections of peak sequences obtained from ChIP-seq or related technologies, RSAT provides a new program (peak-motifs) that combines several efficient motif discovery algorithms to predict transcription factor binding motifs, match them against motif databases and predict their binding sites. Availability (web site, stand-alone programs and SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services): http://rsat.ulb.ac.be/rsat/.
authors.affiliation: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany. morgane@bigre.ulb.ac.be
authors.forename: Morgane
authors.initials: M
authors.lastname: Thomas-Chollier
authors.forename: Matthieu
authors.initials: M
authors.lastname: Defrance
authors.forename: Alejandra
authors.initials: A
authors.lastname: Medina-Rivera
authors.forename: Olivier
authors.initials: O
authors.lastname: Sand
authors.forename: Carl
authors.initials: C
authors.lastname: Herrmann
authors.forename: Denis
authors.initials: D
authors.lastname: Thieffry
authors.forename: Jacques
authors.initials: J
authors.lastname: van Helden
mesh_terms: D001665:Binding Sites; D023281:Genomics; D050436:Regulatory Elements, Transcriptional; D012045:Regulatory Sequences, Nucleic Acid; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors