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噬菌体基因组探索性分析和可视化的交互式网络平台 PhageGE

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

机构信息

Infection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Australia.

Monash Biomedicine Discovery Institute-Wenzhou Medical University Alliance in Clinical and Experimental Biomedicine, Monash University, Clayton 3800, Australia.

出版信息

Gigascience. 2024 Jan 2;13. doi: 10.1093/gigascience/giae074.

DOI:10.1093/gigascience/giae074
PMID:39320317
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11423353/
Abstract

BACKGROUND

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.

FINDINGS

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.

CONCLUSIONS

PhageGE is a valuable tool that simplifies the analysis of phage genome data and may expedite the development and clinical translation of phage therapy. PhageGE is publicly available at https://jason-zhao.shinyapps.io/PhageGE_Update/.

摘要

背景

抗菌药物耐药性是对全球健康的严重威胁。由于抗生素发现管道停滞不前，噬菌体（phages）已被提议作为治疗多药耐药病原体引起的感染的替代疗法。基因组特征在噬菌体药理学中起着重要作用。然而，我们对噬菌体基因组学的了解还很匮乏，并且使用现有的生物信息学管道和工具需要相当多的生物信息学专业知识。这些挑战极大地限制了噬菌体治疗的临床转化。

发现

我们开发了 PhageGE（噬菌体基因组浏览器），这是一个用户友好的图形界面应用程序，用于交互式分析噬菌体基因组。PhageGE 允许用户执行关键分析，包括系统发育分析、系统发育树可视化、噬菌体生命周期预测以及噬菌体基因组注释的比较分析。新的 R Shiny 网络服务器 PhageGE 集成了现有的 R 包，并将它们与几个新开发的功能结合在一起，以方便这些分析。此外，该网络服务器提供交互式可视化功能，并允许用户直接导出具有出版质量的图像。

结论

PhageGE 是一个有价值的工具，它简化了噬菌体基因组数据的分析，可能会加速噬菌体治疗的开发和临床转化。PhageGE 可在 https://jason-zhao.shinyapps.io/PhageGE_Update/ 上公开获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1732/11423353/8d63cf01b380/giae074fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1732/11423353/adcf381eb827/giae074fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1732/11423353/a25fdc62f1f1/giae074fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1732/11423353/a93ae9cb75a8/giae074fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1732/11423353/b30a6daaffed/giae074fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1732/11423353/8d63cf01b380/giae074fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1732/11423353/adcf381eb827/giae074fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1732/11423353/a25fdc62f1f1/giae074fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1732/11423353/a93ae9cb75a8/giae074fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1732/11423353/b30a6daaffed/giae074fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1732/11423353/8d63cf01b380/giae074fig5.jpg

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