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Nat Protoc. 2008;3(10):1578-88. doi: 10.1038/nprot.2008.97.

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

Author information

1
Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles CP 263, Campus Plaine, Boulevard du Triomphe, Bruxelles, Belgium.

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.

PMID:
18802439
DOI:
10.1038/nprot.2008.97
[Indexed for MEDLINE]

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