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


BACKGROUND
The program RNAmicro is available as source code and can be downloaded from http://www.bioinf.uni-leipzig/Software/RNAmicro.
Hertel
Jana
J
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
Stadler
Peter F
PF
D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D017124:Conserved Sequence; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods; D012322:RNA Precursors / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software
D035683:MicroRNAs; D012322:RNA Precursors