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


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2008-09-18

AUTHORS

Jean-Valery Turatsinze, Morgane Thomas-Chollier, Matthieu Defrance, Jacques van Helden

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. More... »

PAGES

1578-1588

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nprot.2008.97

DOI

http://dx.doi.org/10.1038/nprot.2008.97

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1006340595

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18802439


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