MatPred: Computational Identification of Mature MicroRNAs within Novel Pre-MicroRNAs

4Citations
Citations of this article
14Readers
Mendeley users who have this article in their library.

Abstract

Background. MicroRNAs (miRNAs) are short noncoding RNAs integral for regulating gene expression at the posttranscriptional level. However, experimental methods often fall short in finding miRNAs expressed at low levels or in specific tissues. While several computational methods have been developed for predicting the localization of mature miRNAs within the precursor transcript, the prediction accuracy requires significant improvement. Methodology/Principal Findings. Here, we present MatPred, which predicts mature miRNA candidates within novel pre-miRNA transcripts. In addition to the relative locus of the mature miRNA within the pre-miRNA hairpin loop and minimum free energy, we innovatively integrated features that describe the nucleotide-specific RNA secondary structure characteristics. In total, 94 features were extracted from the mature miRNA loci and flanking regions. The model was trained based on a radial basis function kernel/support vector machine (RBF/SVM). Our method can predict precise locations of mature miRNAs, as affirmed by experimentally verified human pre-miRNAs or pre-miRNAs candidates, thus achieving a significant advantage over existing methods. Conclusions. MatPred is a highly effective method for identifying mature miRNAs within novel pre-miRNA transcripts. Our model significantly outperformed three other widely used existing methods. Such processing prediction methods may provide important insight into miRNA biogenesis.

Cite

CITATION STYLE

APA

Li, J., Wang, Y., Wang, L., Feng, W., Luan, K., Dai, X., … Liang, H. (2015). MatPred: Computational Identification of Mature MicroRNAs within Novel Pre-MicroRNAs. BioMed Research International, 2015. https://doi.org/10.1155/2015/546763

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free