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

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.

Findings

We present PPR-Meta, a 3-class classifier that allows simultaneous identification of both phage and plasmid fragments from metagenomic assemblies. PPR-Meta consists of several modules for predicting sequences of different lengths. Using deep learning, a novel network architecture, referred to as the Bi-path Convolutional Neural Network, is des

SUBMITTER: Fang Z 

PROVIDER: S-EPMC6586199 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature