MicroRNAfold: pre-microRNA secondary structure prediction based on modified NCM model with thermodynamics-based scoring strategy Online publication date: Wed, 17-Dec-2014
by Dianwei Han; Jun Zhang; Guiliang Tang
International Journal of Data Mining and Bioinformatics (IJDMB), Vol. 6, No. 3, 2012
Abstract: An accurate prediction of the pre-microRNA secondary structure is important in miRNA informatics. Based on a recently proposed model, nucleotide cyclic motifs (NCM), to predict RNA secondary structure, we propose and implement a Modified NCM (MNCM) model with a physics-based scoring strategy to tackle the problem of pre-microRNA folding. Our microRNAfold is implemented using a global optimal algorithm based on the bottom-up local optimal solutions. Our experimental results show that microRNAfold outperforms the current leading prediction tools in terms of True Negative rate, False Negative rate, Specificity, and Matthews coefficient ratio.
Online publication date: Wed, 17-Dec-2014
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