title: RNAhybrid: microRNA target prediction easy, fast and flexible.
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.
authors.affiliation: Center for Biotechnology, CeBiTec, Universität Bielefeld, 33594 Bielefeld, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Krüger
authors.forename: Marc
authors.initials: M
authors.lastname: Rehmsmeier
mesh_terms: D020413:3' Untranslated Regions / Q000737:chemistry; D000818:Animals; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000235:genetics; D029742:Caenorhabditis elegans Proteins / Q000235:genetics; D018398:Homeodomain Proteins / Q000235:genetics; D020407:Internet; D035683:MicroRNAs / Q000737:chemistry*; D034622:RNA Interference; D012984:Software
chemical_list: D020413:3' Untranslated Regions; D029742:Caenorhabditis elegans Proteins; D018398:Homeodomain Proteins; D035683:MicroRNAs; C108673:lin-39 protein, C elegans