DeephageTP: a convolutional neural network framework for identifying phage-specific proteins from metagenomic sequencing data.

ABSTRACT: Bacteriophages (phages) are the most abundant and diverse biological entity on Earth. Due to the lack of universal gene markers and database representatives, there about 50-90% of genes of phages are unable to assign functions. This makes it a challenge to identify phage genomes and annotate functions of phage genes efficiently by homology search on a large scale, especially for newly phages. Portal (portal protein), TerL (large terminase subunit protein), and TerS (small terminase subunit protein) are three specific proteins of Caudovirales phage. Here, we developed a CNN (convolutional neural network)-based framework, DeephageTP, to identify the three specific proteins from metagenomic data. The framework takes one-hot encoding data of original protein sequences as the input and automati

SUBMITTER: Chu Y 

PROVIDER: S-EPMC9188312 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature