RSAT: regulatory sequence analysis tools Export

@article{citeulike:2825384, 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. 10.1093/nar/gkn304}, author = {Thomas-Chollier, Morgane and Sand, Olivier and Turatsinze, Jean-Valery and Janky, Rekin's and Defrance, Matthieu and Vervisch, Eric and Brohee, Sylvain and van Helden, Jacques}, citeulike-article-id = {2825384}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkn304}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_2/W119}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18495751}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18495751}, day = {21}, doi = {10.1093/nar/gkn304}, journal = {Nucl. Acids Res.}, keywords = {application, comparison, discovery, motif, review}, month = {May}, pages = {gkn304+}, posted-at = {2008-05-23 14:55:45}, priority = {2}, title = {RSAT: regulatory sequence analysis tools}, url = {http://dx.doi.org/10.1093/nar/gkn304}, year = {2008} }

TY - JOUR ID - citeulike:2825384 L3 - citeulike-article-id:2825384 N2 - 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. 10.1093/nar/gkn304 JF - Nucl. Acids Res. TI - RSAT: regulatory sequence analysis tools SP - gkn304 KW - application KW - comparison KW - discovery KW - motif KW - review AU - Thomas-Chollier, Morgane AU - Sand, Olivier AU - Turatsinze, Jean-Valery AU - Janky, Rekin's AU - Defrance, Matthieu AU - Vervisch, Eric AU - Brohee, Sylvain AU - van Helden, Jacques PY - 2008/05/21/ UR - http://dx.doi.org/10.1093/nar/gkn304 ER -