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Nucleic Acids Research Advance Access published online on October 15, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn707
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© 2008 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.

Database Issue

miROrtho: computational survey of microRNA genes

Daniel Gerlach1,2, Evgenia V. Kriventseva1, Nazim Rahman1, Charles E. Vejnar1,2 and Evgeny M. Zdobnov1,2,3,*

1Department of Genetic Medicine and Development, University of Geneva Medical School, 2Swiss Institute of Bioinformatics, 1 Rue Michel-Servet, 1211 Geneva, Switzerland and 3Imperial College London, South Kensington Campus, SW7 2AZ London, UK

*To whom correspondence should be addressed. Tel: +41 22 379 59 73; Fax: +41 22 379 57 06; Email: evgeny.zdobnov{at}unige.ch

Received August 19, 2008. Revised September 26, 2008. Accepted September 29, 2008.

MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature ~22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally validated in vertebrate genomes, yet their discovery remains challenging, and substantially higher numbers have been estimated. The miROrtho database (http://cegg.unige.ch/mirortho) presents the results of a comprehensive computational survey of miRNA gene candidates across the majority of sequenced metazoan genomes. We designed and applied a three-tier analysis pipeline: (i) an SVM-based ab initio screen for potent hairpins, plus homologs of known miRNAs, (ii) an orthology delineation procedure and (iii) an SVM-based classifier of the ortholog multiple sequence alignments. The web interface provides direct access to putative miRNA annotations, ortholog multiple alignments, RNA secondary structure conservation, and sequence data. The miROrtho data are conceptually complementary to the miRBase catalog of experimentally verified miRNA sequences, providing a consistent comparative genomics perspective as well as identifying many novel miRNA genes with strong evolutionary support.


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