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Nucleic Acids Research 2006 34(Web Server issue):W546-W550; doi:10.1093/nar/gkl250
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

jPREdictor: a versatile tool for the prediction of cis-regulatory elements

Thomas Fiedler and Marc Rehmsmeier*

Center for Biotechnology, CeBiTec, Universität Bielefeld 33594 Bielefeld, Germany

*To whom correspondence should be addressed. Tel: +49 0 521 106 2905; Fax: +49 0 521 106 6411; Email: marc{at}techfak.uni-bielefeld.de

Received February 13, 2006. Revised March 29, 2006. Accepted March 30, 2006.

Gene regulation is the process through which an organism effects spatial and temporal differences in gene expression levels. Knowledge of cis-regulatory elements as key players in gene regulation is indispensable for the understanding of the latter and of the development of organisms. Here we present the tool jPREdictor for the fast and versatile prediction of cis-regulatory elements on a genome-wide scale. The prediction is based on clusters of individual motifs and any combination of these into multi-motifs with selectable minimal and maximal distances. Individual motifs can be of heterogenous classes, such as simple sequence motifs or position-specific scoring matrices. Cluster scores are weighted occurrences of multi-motifs, where the weights are derived from positive and negative training sets. We illustrate the flexibility of the jPREdictor with a new predic-tion of Polycomb/Trithorax Response Elements in Drosophila melanogaster. jPREdictor is available as a graphical user interface for online use and for download at http://bibiserv.techfak.uni-bielefeld.de/jpredictor.


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