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Bioinformatics 2006 22(14):e197-e202; doi:10.1093/bioinformatics/btl257
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data

Jana Hertel 1,* and Peter F. Stadler 1,2,3

1 Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig Härtelstraße 16-18, D-04107 Leipzig, Germany
2 Institute for Theoretical Chemistry, University of Vienna Währingerstraße 17, A-1090 Wien, Austria
3 Santa Fe Institute 1399 Hyde Park Rd., Santa Fe, NM 87501, USA

*To whom correspondence should be addressed.

Summary: Recently, genome-wide surveys for non-coding RNAs have provided evidence for tens of thousands of previously undescribed evolutionary conserved RNAs with distinctive secondary structures. The annotation of these putative ncRNAs, however, remains a difficult problem. Here we describe an SVM-based approach that, in conjunction with a non-stringent filter for consensus secondary structures, is capable of efficiently recognizing microRNA precursors in multiple sequence alignments. The software was applied to recent genome-wide RNAz surveys of mammals, urochordates, and nematodes.

Availability: The program RNAmicro is available as source code and can be downloaded from http://www.bioinf.uni-leipzig/Software/RNAmicro

Contact:Jana Hertel, Tel: ++49 341 97 16704, Fax: ++49 341 97 16709, {jana,studla}@bioinf.uni-leipzig.de


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