Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 06-002


Hairpins in a Haystack: Recognizing microRNA Precursors in Comparative Genomics Data

Jana Hertel, Peter F. Stadler,

ISMB 2006

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 a 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 \texttt{RNAz} surveys of mammals, urochordates, and nematodes.

Keywords: miRNA detection, support vector machine classification, miRNA precursor

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Last modified: 2006-03-08 09:22 jana