par Turatsinze, Jean Valéry ;Thomas-Chollier, Morgane ;Defrance, Matthieu ;van Helden, Jacques
Référence Nature Protocols (Online), 3, 10, page (1578-1588)
Publication Publié, 2008
Référence Nature Protocols (Online), 3, 10, page (1578-1588)
Publication Publié, 2008
Article révisé par les pairs
Résumé : | 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. |