RNAhybrid: microRNA target prediction easy, fast, and flexible (2006)
| Venue: | Nucleic Acids Res |
| Citations: | 122 - 3 self |
BibTeX
@ARTICLE{Krüger06rnahybrid:microrna,
author = {Jan Krüger and Marc Rehmsmeier},
title = {RNAhybrid: microRNA target prediction easy, fast, and flexible},
journal = {Nucleic Acids Res},
year = {2006},
pages = {451--454}
}
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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 30-untrans lated region of lin-39. RNAhybrid is available at
Keyphrases
microrna target prediction seed region user-implemented program potential target rnahybrid flexibility base pair non-canonical target site target prediction method useful feature remote call microrna regulatory network 30-untrans lated region flexible online prediction seed-match speed-up
