RNAhybrid: microRNA target prediction easy, fast and flexible

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.