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Open Access Highly Accessed Open Badges Methodology article

Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine

Chenghai Xue12, Fei Li1, Tao He1, Guo-Ping Liu23, Yanda Li1 and Xuegong Zhang1*

Author Affiliations

1 MOE Key Laboratory of Bioinformatics / Department of Automation, Tsinghua University, Beijing 100084, China

2 Laboratory of Complex Systems and Intelligence Science, Institute of Automation, Chinese Academy of Sciences, Beijing 100080, China

3 School of Electronics, University of Glamorgan, Pontypridd CF37 1DL, UK

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BMC Bioinformatics 2005, 6:310  doi:10.1186/1471-2105-6-310

Published: 29 December 2005



MicroRNAs (miRNAs) are a group of short (~22 nt) non-coding RNAs that play important regulatory roles. MiRNA precursors (pre-miRNAs) are characterized by their hairpin structures. However, a large amount of similar hairpins can be folded in many genomes. Almost all current methods for computational prediction of miRNAs use comparative genomic approaches to identify putative pre-miRNAs from candidate hairpins. Ab initio method for distinguishing pre-miRNAs from sequence segments with pre-miRNA-like hairpin structures is lacking. Being able to classify real vs. pseudo pre-miRNAs is important both for understanding of the nature of miRNAs and for developing ab initio prediction methods that can discovery new miRNAs without known homology.


A set of novel features of local contiguous structure-sequence information is proposed for distinguishing the hairpins of real pre-miRNAs and pseudo pre-miRNAs. Support vector machine (SVM) is applied on these features to classify real vs. pseudo pre-miRNAs, achieving about 90% accuracy on human data. Remarkably, the SVM classifier built on human data can correctly identify up to 90% of the pre-miRNAs from other species, including plants and virus, without utilizing any comparative genomics information.


The local structure-sequence features reflect discriminative and conserved characteristics of miRNAs, and the successful ab initio classification of real and pseudo pre-miRNAs opens a new approach for discovering new miRNAs.