About this Journal Submit a Manuscript Table of Contents
Journal of Nucleic Acids
Volume 2010 (2010), Article ID 495904, 10 pages
http://dx.doi.org/10.4061/2010/495904
Research Article

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

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

Received 25 March 2010; Revised 10 June 2010; Accepted 29 June 2010

Academic Editor: Ben Berkhout

Copyright © 2010 Jan-Hendrik Teune and Gerhard Steger. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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).