Identification of bacteriophage genome sequences with representation learning.

ABSTRACT:

Motivation

Bacteriophages/phages are the viruses that infect and replicate within bacteria and archaea, and rich in human body. To investigate the relationship between phages and microbial communities, the identification of phages from metagenome sequences is the first step. Currently, there are two main methods for identifying phages: database-based (alignment-based) methods and alignment-free methods. Database-based methods typically use a large number of sequences as references; alignment-free methods usually learn the features of the sequences with machine learning and deep learning models.

Results

We propose INHERIT which uses a deep representation learning model to integrate both database-based and alignment-free methods, combining the strengths of both. Pre-training i

SUBMITTER: Bai Z 

PROVIDER: S-EPMC9477532 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature