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This article is part of the supplement: APBioNet – Fifth International Conference on Bioinformatics (InCoB2006)

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MicroTar: predicting microRNA targets from RNA duplexes

Rahul Thadani1 and Martti T Tammi123*

Author Affiliations

1 Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543

2 Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597

3 Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden

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BMC Bioinformatics 2006, 7(Suppl 5):S20  doi:10.1186/1471-2105-7-S5-S20

Published: 18 December 2006



The accurate prediction of a comprehensive set of messenger RNAs (targets) regulated by animal microRNAs (miRNAs) remains an open problem. In particular, the prediction of targets that do not possess evolutionarily conserved complementarity to their miRNA regulators is not adequately addressed by current tools.


We have developed MicroTar, an animal miRNA target prediction tool based on miRNA-target complementarity and thermodynamic data. The algorithm uses predicted free energies of unbound mRNA and putative mRNA-miRNA heterodimers, implicitly addressing the accessibility of the mRNA 3' untranslated region. MicroTar does not rely on evolutionary conservation to discern functional targets, and is able to predict both conserved and non-conserved targets. MicroTar source code and predictions are accessible at webcite, where both serial and parallel versions of the program can be downloaded under an open-source licence.


MicroTar achieves better sensitivity than previously reported predictions when tested on three distinct datasets of experimentally-verified miRNA-target interactions in C. elegans, Drosophila, and mouse.