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Updated: May 28, 2026

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

Phamerator: a bioinformatic tool for comparative bacteriophage genomics.

Steven G Cresawn¹, Matt Bogel, Nathan Day

¹Department of Biology, James Madison University, 820 Madison Dr, MSC 7801, Harrisonburg, VA 22807 USA. cresawsg@jmu.edu

BMC Bioinformatics

|October 14, 2011

Summary

Phamerator is a new bioinformatic tool that groups bacteriophage genes into families. This tool aids in comparative genomic analysis and visualizing phage genome relationships.

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Area of Science:

Genomics
Bioinformatics
Microbiology

Background:

Bacteriophage genomes exhibit mosaic architectures.
Many small open reading frames (ORFs) in bacteriophages have unknown functions.
These features pose challenges for annotation, comparative analysis, and representation.

Purpose of the Study:

To introduce Phamerator, a novel bioinformatic tool.
To facilitate the annotation and comparative analysis of bacteriophage genomes.
To enable better representation of phage genomic data.

Main Methods:

Phamerator sorts protein-coding genes into 'phamilies' based on sequence relatedness.
It utilizes pairwise comparisons to build a comprehensive database of gene relationships.
The tool generates genome maps and 'phamily circle' representations.

Main Results:

Phamerator successfully categorizes genes into related families.
Generated genome maps integrate nucleotide and amino acid sequence relationships, and conserved domains.
Phamily circle representations aid in analyzing gene evolutionary histories and horizontal gene transfer.

Conclusions:

Phamerator is an effective tool for comparative genomic analysis of bacteriophages.
It provides valuable comparative representations of bacteriophage genomes.
The tool enhances the understanding of phage genome evolution and gene dynamics.