Ontology type: schema:ScholarlyArticle
2008-09-18
AUTHORSJean-Valery Turatsinze, Morgane Thomas-Chollier, Matthieu Defrance, Jacques van Helden
ABSTRACTThis 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. More... »
PAGES1578-1588
http://scigraph.springernature.com/pub.10.1038/nprot.2008.97
DOIhttp://dx.doi.org/10.1038/nprot.2008.97
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PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/18802439
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