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

IF 11.8 2区生物学 Q1 MULTIDISCIPLINARY SCIENCES

GigaScience Pub Date : 2024-01-02 DOI:10.1093/gigascience/giae074

Jinxin Zhao, Jiru Han, Yu-Wei Lin, Yan Zhu, Michael Aichem, Dimitar Garkov, Phillip J Bergen, Sue C Nang, Jian-Zhong Ye, Tieli Zhou, Tony Velkov, Jiangning Song, Falk Schreiber, Jian Li

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引用次数: 0

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/.

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PhageGE：噬菌体基因组探索性分析和可视化互动网络平台。

背景：抗菌药耐药性是对全球健康的严重威胁。由于抗生素的研发停滞不前，噬菌体（phage）被提议作为治疗耐多药病原体感染的替代疗法。基因组特征在噬菌体药理学中发挥着重要作用。然而，我们对噬菌体基因组学的了解并不多，使用现有的生物信息学管道和工具需要大量的生物信息学专业知识。这些挑战极大地限制了噬菌体疗法的临床转化：我们开发了 PhageGE（噬菌体基因组资源管理器），这是一款用户友好型图形界面应用程序，用于交互式分析噬菌体基因组。PhageGE使用户能够进行关键分析，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比较分析。新的 R Shiny 网络服务器 PhageGE 整合了现有的 R 软件包，并将它们与几个新开发的功能相结合，为这些分析提供了便利。此外，网络服务器还提供交互式可视化功能，并允许用户直接导出出版物质量的图像：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，可能会加快噬菌体疗法的开发和临床转化。PhageGE 可通过 https://jason-zhao.shinyapps.io/PhageGE_Update/ 公开获取。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

GigaScience MULTIDISCIPLINARY SCIENCES-

CiteScore

15.50

自引率

1.10%

发文量

119

审稿时长

1 weeks

期刊介绍： GigaScience seeks to transform data dissemination and utilization in the life and biomedical sciences. As an online open-access open-data journal, it specializes in publishing "big-data" studies encompassing various fields. Its scope includes not only "omic" type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale shareable data.