Title: MicroRNAfold: pre-microRNA secondary structure prediction based on modified NCM model with thermodynamics-based scoring strategy

Authors: Dianwei Han; Jun Zhang; Guiliang Tang

Addresses: Department of Computer Science, University of Kentucky, Lexington, KY 40506-0046, USA ' Department of Computer Science, University of Kentucky, Lexington, KY 40506-0046, USA ' Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0236, USA

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.

Keywords: thermodynamics; scoring function; RNA folding; pre-microRNA secondary structure prediction; bottom-up local optimal solutions; NCM model; nucleotide cyclic motifs; scoring strategy; bioinformatics.

DOI: 10.1504/IJDMB.2012.049246

International Journal of Data Mining and Bioinformatics, 2012 Vol.6 No.3, pp.272 - 291

Received: 05 Oct 2009
Accepted: 22 Jul 2010
Published online: 17 Dec 2014 *

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