A guide through present computational approaches for the identification of mammalian microRNA targets

Nat Methods. 2006 Nov;3(11):881-6. doi: 10.1038/nmeth954.


Computational microRNA (miRNA) target prediction is a field in flux. Here we present a guide through five widely used mammalian target prediction programs. We include an analysis of the performance of these individual programs and of various combinations of these programs. For this analysis we compiled several benchmark data sets of experimentally supported miRNA-target gene interactions. Based on the results, we provide a discussion on the status of target prediction and also suggest a stepwise approach toward predicting and selecting miRNA targets for experimental testing.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • 3' Untranslated Regions / genetics
  • 5' Untranslated Regions / genetics
  • Animals
  • Computational Biology / methods*
  • Gene Targeting / methods*
  • Humans
  • MicroRNAs / genetics*
  • Predictive Value of Tests
  • RNA, Messenger / genetics
  • Sensitivity and Specificity
  • Software*


  • 3' Untranslated Regions
  • 5' Untranslated Regions
  • MicroRNAs
  • RNA, Messenger