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Open Access Highly Accessed Methodology article

miRFam: an effective automatic miRNA classification method based on n-grams and a multiclass SVM

Jiandong Ding12, Shuigeng Zhou12* and Jihong Guan3*

Author Affiliations

1 School of Computer Science, Fudan University, Shanghai 200433, China

2 Shanghai Key Lab of Intelligent Information Processing, Shanghai 200433, China

3 Department of Computer Science & Technology, Tongji University, Shanghai 200433, China

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BMC Bioinformatics 2011, 12:216  doi:10.1186/1471-2105-12-216

Published: 28 May 2011

Abstract

Background

MicroRNAs (miRNAs) are ~22 nt long integral elements responsible for post-transcriptional control of gene expressions. After the identification of thousands of miRNAs, the challenge is now to explore their specific biological functions. To this end, it will be greatly helpful to construct a reasonable organization of these miRNAs according to their homologous relationships. Given an established miRNA family system (e.g. the miRBase family organization), this paper addresses the problem of automatically and accurately classifying newly found miRNAs to their corresponding families by supervised learning techniques. Concretely, we propose an effective method, miRFam, which uses only primary information of pre-miRNAs or mature miRNAs and a multiclass SVM, to automatically classify miRNA genes.

Results

An existing miRNA family system prepared by miRBase was downloaded online. We first employed n-grams to extract features from known precursor sequences, and then trained a multiclass SVM classifier to classify new miRNAs (i.e. their families are unknown). Comparing with miRBase's sequence alignment and manual modification, our study shows that the application of machine learning techniques to miRNA family classification is a general and more effective approach. When the testing dataset contains more than 300 families (each of which holds no less than 5 members), the classification accuracy is around 98%. Even with the entire miRBase15 (1056 families and more than 650 of them hold less than 5 samples), the accuracy surprisingly reaches 90%.

Conclusions

Based on experimental results, we argue that miRFam is suitable for application as an automated method of family classification, and it is an important supplementary tool to the existing alignment-based small non-coding RNA (sncRNA) classification methods, since it only requires primary sequence information.

Availability

The source code of miRFam, written in C++, is freely and publicly available at: http://admis.fudan.edu.cn/projects/miRFam.htm webcite.