title: Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.
abstract: This protocol shows how to detect putative cis-regulatory elements and regions enriched in such elements with the regulatory sequence analysis tools (RSAT) web server (http://rsat.ulb.ac.be/rsat/). The approach applies to known transcription factors, whose binding specificity is represented by position-specific scoring matrices, using the program matrix-scan. The detection of individual binding sites is known to return many false predictions. However, results can be strongly improved by estimating P value, and by searching for combinations of sites (homotypic and heterotypic models). We illustrate the detection of sites and enriched regions with a study case, the upstream sequence of the Drosophila melanogaster gene even-skipped. This protocol is also tested on random control sequences to evaluate the reliability of the predictions. Each task requires a few minutes of computation time on the server. The complete protocol can be executed in about one hour.
authors.affiliation: Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles CP 263, Campus Plaine, Boulevard du Triomphe, Bruxelles, Belgium.
authors.forename: Jean-Valery
authors.initials: JV
authors.lastname: Turatsinze
authors.forename: Morgane
authors.initials: M
authors.lastname: Thomas-Chollier
authors.forename: Matthieu
authors.initials: M
authors.lastname: Defrance
authors.forename: Jacques
authors.initials: J
authors.lastname: van Helden
mesh_terms: D001665:Binding Sites / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence / Q000235:genetics; D005821:Genetic Techniques; D023281:Genomics / Q000379:methods*; D009841:Oligonucleotides / Q000235:genetics; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D012984:Software; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D009841:Oligonucleotides; D014157:Transcription Factors