DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach.

Journal: GigaScience
Published Date: Sep 8, 2021

Abstract

BACKGROUND: Prokaryotic viruses referred to as phages can be divided into virulent and temperate phages. Distinguishing virulent and temperate phage-derived sequences in metavirome data is important for elucidating their different roles in interactions with bacterial hosts and regulation of microbial communities. However, there is no experimental or computational approach to effectively classify their sequences in culture-independent metavirome. We present a new computational method, DeePhage, which can directly and rapidly judge each read or contig as a virulent or temperate phage-derived fragment.

Authors

  • Shufang Wu
    State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China.
  • Zhencheng Fang
    State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China.
  • Jie Tan
    Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
  • Mo Li
    School of Computer Science and Engineering, Key Laboratory of Big Data Management and Analytics (Liaoning), Northeastern University, China.
  • Chunhui Wang
    State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering and Center for Quantitative Biology, Peking University, Beijing 100871, China.
  • Qian Guo
    State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, Beijing, China.
  • Congmin Xu
    State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China.
  • Xiaoqing Jiang
    State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, Beijing, China.
  • Huaiqiu Zhu
    Department of Biomedical Engineering, College of Engineering, and Centre for Quantitative Biology, Peking University, Beijing, China.

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