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Updated: Sep 26, 2025

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

DEPhT: a novel approach for efficient prophage discovery and precise extraction.

Christian H Gauthier¹, Lawrence Abad¹, Ananya K Venbakkam¹

¹Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.

Nucleic Acids Research

|April 22, 2022

Summary

A new tool, DEPhT, aids in identifying and extracting prophages from bacterial genomes. Prophages are common in Mycobacterium but notably absent in all sequenced Mycobacterium tuberculosis strains.

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Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

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Published on: June 11, 2015

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Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

Area of Science:

Microbiology
Genomics
Bioinformatics

Background:

Bacterial genomes frequently contain integrated prophages from temperate bacteriophages.
Prophages influence bacterial traits like metabolism, pathogenicity, and antibiotic resistance.
Computational identification and precise extraction of prophages for analysis are challenging.

Purpose of the Study:

To introduce DEPhT, a multimodal tool for prophage discovery and extraction.
To enable efficient screening of large bacterial genome datasets.
To facilitate precise prophage sequence extraction and annotation.

Main Methods:

DEPhT utilizes genomic architectural features to distinguish phage from bacterial DNA for discovery.
Targeted homology searches are employed for precise prophage sequence extraction.
The tool offers three distinct run modes for comprehensive analysis.

Main Results:

DEPhT was developed for Mycobacterium genomes but is adaptable to other bacteria.
Prophages are prevalent across various Mycobacterium strains.
Notably, prophages were found to be absent in all sequenced Mycobacterium tuberculosis strains.

Conclusions:

DEPhT is an effective tool for prophage identification and extraction in bacterial genomics.
The study reveals a significant absence of prophages in Mycobacterium tuberculosis.
This finding has implications for understanding the evolution and biology of Mycobacterium tuberculosis.