RNAhybrid: microRNA target prediction easy, fast and flexible

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W451-4. doi: 10.1093/nar/gkl243.


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.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions / chemistry
  • Animals
  • Binding Sites
  • Caenorhabditis elegans / genetics
  • Caenorhabditis elegans Proteins / genetics
  • Homeodomain Proteins / genetics
  • Internet
  • MicroRNAs / chemistry*
  • RNA Interference*
  • Software*


  • 3' Untranslated Regions
  • Caenorhabditis elegans Proteins
  • Homeodomain Proteins
  • MicroRNAs
  • lin-39 protein, C elegans