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This article is part of the supplement: Proceedings of the Third Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2013)

Open Access Proceedings

Gene prediction in metagenomic fragments based on the SVM algorithm

Yongchu Liu12, Jiangtao Guo12, Gangqing Hu124 and Huaiqiu Zhu123*

Author Affiliations

1 State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China

2 Center for Theoretical Biology, Peking University, Beijing 100871, China

3 Center for Protein Science, Peking University, Beijing 100871, China

4 Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA

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BMC Bioinformatics 2013, 14(Suppl 5):S12  doi:10.1186/1471-2105-14-S5-S12

Published: 10 April 2013

Abstract

Background

Metagenomic sequencing is becoming a powerful technology for exploring micro-ogranisms from various environments, such as human body, without isolation and cultivation. Accurately identifying genes from metagenomic fragments is one of the most fundamental issues.

Results

In this article, we present a novel gene prediction method named MetaGUN for metagenomic fragments based on a machine learning approach of SVM. It implements in a three-stage strategy to predict genes. Firstly, it classifies input fragments into phylogenetic groups by a k-mer based sequence binning method. Then, protein-coding sequences are identified for each group independently with SVM classifiers that integrate entropy density profiles (EDP) of codon usage, translation initiation site (TIS) scores and open reading frame (ORF) length as input patterns. Finally, the TISs are adjusted by employing a modified version of MetaTISA. To identify protein-coding sequences, MetaGun builds the universal module and the novel module. The former is based on a set of representative species, while the latter is designed to find potential functionary DNA sequences with conserved domains.

Conclusions

Comparisons on artificial shotgun fragments with multiple current metagenomic gene finders show that MetaGUN predicts better results on both 3' and 5' ends of genes with fragments of various lengths. Especially, it makes the most reliable predictions among these methods. As an application, MetaGUN was used to predict genes for two samples of human gut microbiome. It identifies thousands of additional genes with significant evidences. Further analysis indicates that MetaGUN tends to predict more potential novel genes than other current metagenomic gene finders.