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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
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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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