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Updated: Jan 15, 2026

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

Empathi: embedding-based phage protein annotation tool by hierarchical assignment.

Alexandre Boulay^1,2, Audrey Leprince³, François Enault⁴

¹Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, QC, Canada. alexandreboulay@outlook.com.

Nature Communications

|October 14, 2025

Summary

This summary is machine-generated.

Bacteriophages (viruses that infect bacteria) have many unknown protein functions. A new tool, Empathi, uses protein embeddings to classify these functions, significantly improving annotation accuracy and understanding phage roles in ecosystems.

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Area of Science:

Microbiology
Bioinformatics
Virology

Background:

Bacteriophages are abundant viruses crucial to microbial ecosystems.
Rapid evolution of bacteriophages results in many proteins with unknown functions.
Existing methods for phage protein function identification lack sensitivity or specificity.

Purpose of the Study:

To introduce Empathi, a novel protein-embedding-based classifier for hierarchical phage protein function assignment.
To develop new, hierarchically organized functional categories for phage proteins suitable for machine learning.

Main Methods:

Empathi utilizes protein embeddings for function classification.
Hierarchical functional categories were specifically designed for phage proteins.
Performance was evaluated on cultured phage genomes and the EnVhogDB database.

Main Results:

Empathi significantly outperforms homology-based methods in annotating phage protein functions.
It tripled the number of annotated homologous groups on cultured phage genomes.
Empathi doubled the annotated fraction of protein families in the EnVhogDB database (from 16% to 33%).

Conclusions:

Empathi provides a more sensitive and specific method for identifying phage protein functions.
Improved functional annotation enhances understanding of phage biology and their interactions with bacteria.
This tool aids in deciphering the functional repertoire of phages in various ecosystems.