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Journal of Biomedicine and Biotechnology
Volume 2006 (2006), Article ID 95270, 10 pages
http://dx.doi.org/10.1155/JBB/2006/95270
Review Article

Computational Prediction of MicroRNAs Encoded in Viral and Other Genomes

1Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, Oslo 0027, Norway
2Department of Immunology, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Centre, Oslo 0310, Norway
3Department of Informatics, University of Oslo, PO Box 1080 Blindern, Oslo 0316, Norway

Received 1 February 2006; Revised 5 April 2006; Accepted 2 May 2006

Copyright © 2006 Gard O. S. Thomassen et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We present an overview of selected computational methods for microRNA prediction. It is especially aimed at viral miRNA detection. As the number of microRNAs increases and the range of genomes encoding miRNAs expands, it seems that these small regulators have a more important role than has been previously thought. Most microRNAs have been detected by cloning and Northern blotting, but experimental methods are biased towards abundant microRNAs as well as being time-consuming. Computational detection methods must therefore be refined to serve as a faster, better, and more affordable method for microRNA detection. We also present data from a small study investigating the problems of computational miRNA prediction. Our findings suggest that the prediction of microRNA precursor candidates is fairly easy, while excluding false positives as well as exact prediction of the mature microRNA is hard. Finally, we discuss possible improvements to computational microRNA detection.