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Nucleic Acids Research 2006 34(Web Server issue):W451-W454; doi:10.1093/nar/gkl243
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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

RNAhybrid: microRNA target prediction easy, fast and flexible

Jan Krüger 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 14, 2006. Revised March 28, 2006. Accepted March 29, 2006.

In the elucidation of the microRNA regulatory network, knowledge of potential targets is of highest importance. Among existing target prediction methods, RNAhybrid [M. Rehmsmeier, P. Steffen, M. Höchsmann and R. Giegerich (2004) RNA, 10, 1507–1517] is unique in offering a flexible online prediction. Recently, some useful features have been added, among these the possibility to disallow G:U base pairs in the seed region, and a seed-match speed-up, which accelerates the program by a factor of 8. In addition, the program can now be used as a webservice for remote calls from user-implemented programs. We demonstrate RNAhybrid's flexibility with the prediction of a non-canonical target site for Caenorhabditis elegans miR-241 in the 3'-untranslated region of lin-39. RNAhybrid is available at http://bibiserv.techfak.uni-bielefeld.de/rnahybrid.


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