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

Abstract EN

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).