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J Nucleic Acids. 2010 Sep 13;2010. pii: 495904. doi: 10.4061/2010/495904.

NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome.

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1
Institut für Physikalische Biologie, Universitätsstr. 1, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.

Abstract

MicroRNAs (miRNA) are small regulatory, noncoding RNA molecules that are transcribed as primary miRNAs (pri-miRNA) from eukaryotic genomes. At least in plants, their regulatory activity is mediated through base-pairing with protein-coding messenger RNAs (mRNA) followed by mRNA degradation or translation repression. We describe NOVOMIR, a program for the identification of miRNA genes in plant genomes. It uses a series of filter steps and a statistical model to discriminate a pre-miRNA from other RNAs and does rely neither on prior knowledge of a miRNA target nor on comparative genomics. The sensitivity and specificity of NOVOMIR for detection of premiRNAs from Arabidopsis thaliana is ~0.83 and ~0.99, respectively. Plant pre-miRNAs are more heterogeneous with respect to size and structure than animal pre-miRNAs. Despite these difficulties, NOVOMIR is well suited to perform searches for pre-miRNAs on a genomic scale. NOVOMIR is written in Perl and relies on two additional, free programs for prediction of RNA secondary structure (RNALFOLD, RNASHAPES).

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