PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning.

Journal: GigaScience
Published Date: Jun 1, 2019

Abstract

BACKGROUND: Phages and plasmids are the major components of mobile genetic elements, and fragments from such elements generally co-exist with chromosome-derived fragments in sequenced metagenomic data. However, there is a lack of efficient methods that can simultaneously identify phages and plasmids in metagenomic data, and the existing tools identifying either phages or plasmids have not yet presented satisfactory performance.

Authors

  • 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.
  • 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.
  • Mo Li
    School of Computer Science and Engineering, Key Laboratory of Big Data Management and Analytics (Liaoning), Northeastern University, 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.
  • Zhongjie Xie
    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.
  • Huaiqiu Zhu
    Department of Biomedical Engineering, College of Engineering, and Centre for Quantitative Biology, Peking University, Beijing, China.

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