NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome
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 transla...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2010-01-01
|
| Series: | Journal of Nucleic Acids |
| Online Access: | http://dx.doi.org/10.4061/2010/495904 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Summary: | 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). |
|---|---|
| ISSN: | 2090-021X |