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Nucleic Acids Research Advance Access originally published online on March 18, 2009
Nucleic Acids Research 2009 37(8):2419-2433; doi:10.1093/nar/gkp145
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Nucleic Acids Research, 2009, Vol. 37, No. 8 2419-2433
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Survey and Summary

Current tools for the identification of miRNA genes and their targets

N. D. Mendes1,2,3,*, A. T. Freitas2 and M.-F. Sagot1,3

1Équipe BAOBAB, Laboratoire de Biométrie et Biologie Évolutive (UMR 5558), CNRS, Univ. Lyon 1, 43 bd du 11 nov 1918, 69622, Villeurbanne Cedex, France, 2INESC-ID/IST, 9 Rua Alves Redol, 1000-029 Lisbon, Portugal and 3BAMBOO Team, INRIA Rhone-Alpes, 655 avenue de l'E;urope, 38330 Montbonnot Saint-Martin, France

*To whom correspondence should be addressed. Tel: +351 21 3100300; Fax: +351 21 3145843; Email: ndm{at}kdbio.inesc-id.pt

Received November 28, 2008. Revised February 16, 2009. Accepted February 18, 2009.

The discovery of microRNAs (miRNAs), almost 10 years ago, changed dramatically our perspective on eukaryotic gene expression regulation. However, the broad and important functions of these regulators are only now becoming apparent. The expansion of our catalogue of miRNA genes and the identification of the genes they regulate owe much to the development of sophisticated computational tools that have helped either to focus or interpret experimental assays. In this article, we review the methods for miRNA gene finding and target identification that have been proposed in the last few years. We identify some problems that current approaches have not yet been able to overcome and we offer some perspectives on the next generation of computational methods.


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