PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations

Ruo Han Wang; Shuo Yang; Zhixuan Liu; Yuanzheng Zhang; Xueying Wang; Zixin Xu; Jianping Wang; Shuai Cheng Li

doi:10.1093/nar/gkad979

PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations

Ruo Han Wang (Co-first Author), Shuo Yang (Co-first Author), Zhixuan Liu, Yuanzheng Zhang, Xueying Wang, Zixin Xu, Jianping Wang^*, Shuai Cheng Li^*

^*Corresponding author for this work

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

111 Citations (Scopus)

177 Downloads (CityUHK Scholars)

Abstract

Bacteriophages are viruses that infect bacteria or archaea. Understanding the diverse and intricate genomic architectures of phages is essential to study microbial ecosystems and develop phage therapy strategies. However, the existing phage databases are short of meticulous annotations. To this end, we propose PhageScope (https://phagescope.deepomics.org), an online phage database with comprehensive annotations. PhageScope harbors a collection of 873 718 phage sequences from various sources. Applying fifteen state-of-the-art tools to perform systematic annotations and analyses, PhageScope provides annotations on genome completeness, host range, lifestyle information, taxonomy classification, nine types of structural and functional genetic elements, and three types of comparative genomic studies for curated phages. Additionally, PhageScope incorporates automatic analyses and visualizations for curated and customized phages, serving as an efficient platform for phage study. © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.

Original language	English
Pages (from-to)	D756–D761
Journal	Nucleic acids research
Volume	52
Issue number	D1
Online published	30 Oct 2023
DOIs	https://doi.org/10.1093/nar/gkad979
Publication status	Published - 5 Jan 2024

Bibliographical note

Research Unit(s) information for this publication is provided by the author(s) concerned.

Funding

Hong Kong Innovation and Technology Fund [GHX/002/19SZ (CityU: 9440262 to S.C.L.)]. Funding for open access charge: Hong Kong Innovation and Technology Fund [GHX/002/19SZ (CityU: 9440262 to S.C.L.)].

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This full text is made available under CC-BY-NC 4.0. https://creativecommons.org/licenses/by-nc/4.0/

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AU - Yang, Shuo

AU - Liu, Zhixuan

AU - Zhang, Yuanzheng

AU - Wang, Xueying

AU - Xu, Zixin

AU - Wang, Jianping

AU - Li, Shuai Cheng

N1 - Research Unit(s) information for this publication is provided by the author(s) concerned.

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AB - Bacteriophages are viruses that infect bacteria or archaea. Understanding the diverse and intricate genomic architectures of phages is essential to study microbial ecosystems and develop phage therapy strategies. However, the existing phage databases are short of meticulous annotations. To this end, we propose PhageScope (https://phagescope.deepomics.org), an online phage database with comprehensive annotations. PhageScope harbors a collection of 873 718 phage sequences from various sources. Applying fifteen state-of-the-art tools to perform systematic annotations and analyses, PhageScope provides annotations on genome completeness, host range, lifestyle information, taxonomy classification, nine types of structural and functional genetic elements, and three types of comparative genomic studies for curated phages. Additionally, PhageScope incorporates automatic analyses and visualizations for curated and customized phages, serving as an efficient platform for phage study. © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.

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PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations

Abstract

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ITF: Algorithms for Gut Microbiome Strains and Structure Variations based on stLFR Sequencing

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PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations

Abstract

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ITF: Algorithms for Gut Microbiome Strains and Structure Variations based on stLFR Sequencing

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