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DNA Bacteriophages

DNA Bacteriophages

Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...

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Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

pdm_utils: a SEA-PHAGES MySQL phage database management toolkit.

Travis N Mavrich¹, Christian Gauthier¹, Lawrence Abad¹

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

Bioinformatics (Oxford, England)

|November 23, 2020

Summary

Bacteriophages (phages) are abundant microbes. A new tool, pdm_utils, aids in managing and analyzing their rapidly growing genomic data for biological discovery.

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Last Updated: Nov 29, 2025

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

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Published on: June 11, 2015

Application of the Intelligent High-Throughput Antimicrobial Sensitivity Testing/Phage Screening System and Lar Index of Antimicrobial Resistance

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

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
Bioinformatics
Genomics

Background:

Bacteriophages (phages) are highly abundant and genetically diverse microorganisms.
The volume of phage genomics data is rapidly increasing, particularly through programs like SEA-PHAGES.
Analyzing this expanding dataset offers significant opportunities for novel biological insights.

Purpose of the Study:

To address the growing need for effective storage, updating, exploration, and analysis of phage genomics data.
To provide a specialized software tool tailored for phage genomics data management.

Main Methods:

Development of the pdm_utils Python package.
Implementation of tools for MySQL phage database management.
Focus on meeting the specific needs of the SEA-PHAGES program and broader phage genomics research.

Main Results:

A collection of tools for MySQL phage database management is now available.
The pdm_utils package facilitates efficient handling of large-scale phage genomic datasets.
The tool supports comparative genomic and bioinformatic analyses.

Conclusions:

The pdm_utils package provides essential functionalities for managing and analyzing phage genomics data.
This tool supports the ongoing discovery of biological insights from the expanding phage genomic landscape.
It is a valuable resource for researchers involved in phage biology and genomics.