PlantMirP-Rice: An Efficient Program for Rice Pre-miRNA Prediction
Open Access
- 17 June 2020
- Vol. 11 (6), 662
- https://doi.org/10.3390/genes11060662
Abstract
Rice microRNAs (miRNAs) are important post-transcriptional regulation factors and play vital roles in many biological processes, such as growth, development, and stress resistance. Identification of these molecules is the basis of dissecting their regulatory functions. Various machine learning techniques have been developed to identify precursor miRNAs (pre-miRNAs). However, no tool is implemented specifically for rice pre-miRNAs. This study aims at improving prediction performance of rice pre-miRNAs by constructing novel features with high discriminatory power and developing a training model with species-specific data. PlantMirP-rice, a stand-alone random forest-based miRNA prediction tool, achieves a promising accuracy of 93.48% based on independent (unseen) rice data. Comparisons with other competitive pre-miRNA prediction methods demonstrate that plantMirP-rice performs better than existing tools for rice and other plant pre-miRNA classification.Funding Information
- National Natural Science Foundation of China (31601071, 11675060)
This publication has 33 references indexed in Scilit:
- Osa-miR164a targets OsNAC60 and negatively regulates rice immunity against the blast fungus Magnaporthe oryzaeThe Plant Journal, 2018
- The OsmiR396c‐OsGRF4‐OsGIF1 regulatory module determines grain size and yield in ricePlant Biotechnology Journal, 2016
- Blocking miR396 increases rice yield by shaping inflorescence architectureNature Plants, 2015
- Prediction of plant pre-microRNAs and their microRNAs in genome-scale sequences using structure-sequence features and support vector machineBMC Bioinformatics, 2014
- Emerging roles of microRNAs in the mediation of drought stress response in plantsJournal of Experimental Botany, 2013
- NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-GenomeJournal of Nucleic Acids, 2010
- Origin, Biogenesis, and Activity of Plant MicroRNAsCell, 2009
- Functions of microRNAs and related small RNAs in plantsNature Genetics, 2006
- A Plant miRNA Contributes to Antibacterial Resistance by Repressing Auxin SignalingScience, 2006
- MicroRNAs: small RNAs with a big role in gene regulationNature Reviews Genetics, 2004