Using RSAT to scan genome sequences for transcription factor binding sites and cis -regulatory modules

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.