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Bioinformatics Advance Access originally published online on September 29, 2009
Bioinformatics 2009 25(23):3049-3055; doi:10.1093/bioinformatics/btp565
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Lost in translation: an assessment and perspective for computational microRNA target identification

Panagiotis Alexiou 1,*, Manolis Maragkakis 1, Giorgos L. Papadopoulos 1, Martin Reczko 1,2 and Artemis G. Hatzigeorgiou 1,3

1 Institute of Molecular Oncology, Biomedical Sciences Research Center ‘Alexander Fleming’, 166 72 Varkiza, Greece, 2 Synaptic Ltd., 700 13 Heraklion, Greece and 3 Computer and Information Sciences, University of Pennsylvania, 19104-6391 Philadelphia, USA

* To whom correspondence should be addressed.


  Abstract

MicroRNAs (miRNAs) are a class of short endogenously expressed RNA molecules that regulate gene expression by binding directly to the messenger RNA of protein coding genes. They have been found to confer a novel layer of genetic regulation in a wide range of biological processes. Computational miRNA target prediction remains one of the key means used to decipher the role of miRNAs in development and disease. Here we introduce the basic idea behind the experimental identification of miRNA targets and present some of the most widely used computational miRNA target identification programs. The review includes an assessment of the prediction quality of these programs and their combinations.

Contact: p.alexiou{at}fleming.gr

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Jonathan Wren

Received on June 16, 2009; revised on September 24, 2009; accepted on September 27, 2009

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