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Bioinformatics. 2006 Jul 15;22(14):e197-202.

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

Author information

1
Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany. jana@bioinf.uni-leipzig.de

Abstract

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.

PMID:
16873472
DOI:
10.1093/bioinformatics/btl257
[Indexed for MEDLINE]

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