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. Hochsmann 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 30- untranslated region of lin-39. RNAhybrid is available at http://bibiserv.techfak.uni-bielefeld.de/rnahybrid.