PhageGE an interactive web platform for exploratory analysis and visualization of bacteriophage genomes
Antimicrobial resistance is a serious threat to global health. Due to the stagnant antibiotic discovery pipeline, bacteriophages (phages) have been proposed as an alternative therapy for the treatment of infections caused by multidrug-resistant pathogens. Genomic features play an important role in phage pharmacology. However, our knowledge of phage genomics is sparse, and the use of existing bioinformatic pipelines and tools requires considerable bioinformatic expertise. These challenges have substantially limited the clinical translation of phage therapy. We have developed PhageGE (Phage Genome Explorer), a user-friendly graphical interface application for the interactive analysis of phage genomes. PhageGE enables users to perform key analyses, including phylogenetic analysis, visualization of phylogenetic trees, prediction of phage life cycle, and comparative analysis of phage genome annotations. The new R Shiny web server, PhageGE, integrates existing R packages and combines them with several newly developed functions to facilitate these analyses. Additionally, the web server provides interactive visualization capabilities and allows users to directly export publication-quality images.
Citation
@article{zhao2024,
author = {Zhao, Jinxin and Han, Jiru and Lin, Yu-Wei and Zhu, Yan and
Aichem, Michael and Garkov, Dimitar and J Bergen, Phillip and C
Nang, Sue and Ye, Jian-Zhong and Zhou, Tieli and Velkov, Tony and
Song, Jiangning and Schreiber, Falk and Li, Jian},
title = {PhageGE an Interactive Web Platform for Exploratory Analysis
and Visualization of Bacteriophage Genomes},
journal = {GigaScience},
volume = {13},
date = {2024-09-25},
url = {https://doi.org/10.1093/gigascience/giae074},
doi = {10.1093/gigascience/giae074},
langid = {en},
abstract = {Antimicrobial resistance is a serious threat to global
health. Due to the stagnant antibiotic discovery pipeline,
bacteriophages (phages) have been proposed as an alternative therapy
for the treatment of infections caused by multidrug-resistant
pathogens. Genomic features play an important role in phage
pharmacology. However, our knowledge of phage genomics is sparse,
and the use of existing bioinformatic pipelines and tools requires
considerable bioinformatic expertise. These challenges have
substantially limited the clinical translation of phage therapy. We
have developed PhageGE (Phage Genome Explorer), a user-friendly
graphical interface application for the interactive analysis of
phage genomes. PhageGE enables users to perform key analyses,
including phylogenetic analysis, visualization of phylogenetic
trees, prediction of phage life cycle, and comparative analysis of
phage genome annotations. The new R Shiny web server, PhageGE,
integrates existing R packages and combines them with several newly
developed functions to facilitate these analyses. Additionally, the
web server provides interactive visualization capabilities and
allows users to directly export publication-quality images.}
}