RNAhybrid: microRNA target prediction easy, fast and flexible

J Krüger, M Rehmsmeier - Nucleic acids research, 2006 - academic.oup.com
J Krüger, M Rehmsmeier
Nucleic acids research, 2006academic.oup.com
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 …
Abstract
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 .
Oxford University Press