PhageGE: an interactive web platform for exploratory analysis and visualization of bacteriophage genomes

Area of Science:

• Genomics
• Bioinformatics
• Microbiology

Background:

• Antimicrobial resistance (AMR) poses a significant global health threat.
• Bacteriophages (phages) are emerging as a therapeutic alternative for multidrug-resistant infections.
• Limited understanding of phage genomics and complex bioinformatic tools hinder phage therapy's clinical application.

Purpose of the Study:

• To develop a user-friendly application for interactive phage genome analysis.
• To streamline key genomic analyses for bacteriophages.
• To facilitate the clinical translation of phage therapy.

Main Methods:

• Development of PhageGE, a graphical interface application built on R Shiny.
• Integration of existing R packages with novel functions for phage genome analysis.
• Implementation of interactive visualization and publication-quality image export features.

Main Results:

• PhageGE enables phylogenetic analysis, life cycle prediction, and comparative genome annotation.
• The application provides interactive visualization of phylogenetic trees.
• Users can easily export high-quality images for research and publication.

Conclusions:

• PhageGE simplifies complex phage genome data analysis.
• The tool has the potential to accelerate the development and clinical adoption of phage therapy.
• PhageGE is accessible online for public use.