PhageScope: A new web-based tool for decoding the phage genome

In the dynamic realm of bioinformatics, a transformative tool has emerged to unravel the intricacies of bacteriophages. PhageScope, a cutting-edge web-based tool developed by scientists from City University of Hong Kong, beckons researchers into the fascinating world of phage genomics. In this in-depth exploration, we delve into the nuances of PhageScope's methodology, applaud its novel features, and scrutinize its performance, all through the lens of an enthusiast.

The Heart of PhageScope's Power

At the core of PhageScope lies a colossal dataset comprising 873,718 phage sequences meticulously curated from public repositories and datasets, a testament to the tool's commitment to exhaustiveness. The journey begins with an exhaustive search across RefSeq, Genbank, EMBL, and DDBJ, coupled with keyword mining and the integration of diverse datasets like PhagesDB and IMG/VR. This meticulous curation culminates in a dataset ripe for exploration.

The Capabilities of PhageScope

Genome Annotation

  1. Completeness Assessment
  2. Phenotype Annotation
    • Host Assignment
    • Lifestyle Prediction
  3. Structural Annotation
    • ORF Prediction & Protein Classification
    • Transcription Terminator Annotation
  4. Taxonomic Annotation
  5. Functional Annotation
    • tRNA & tmRNA Gene Annotation
    • Anti-CRISPR Protein Annotation
    • CRISPR Array Annotation
    • Virulent Factor & Antimicrobial Resistance Gene Detection
    • Transmembrane Protein Annotation

Genome Comparison

  1. Sequence Clustering
  2. Sequence Alignment
  3. Comparative Tree Construction

Genome Annotation

A snapshot of linearized genome annotation on PhageScope
A snapshot of linearized genome annotation on PhageScope

PhageScope's strength lies not just in the dataset but in its application of state-of-the-art tools for systematic genome annotations. The completeness assessment, a critical step, employs CheckV v0.8.1 to categorize genomes into tiers, ensuring users navigate a landscape of reliable data. The phenotype annotation, a nuanced dance between DeepHost and homology searches, not only assigns host taxonomies but also predicts the elusive phage lifestyles. Structural annotation, a complex orchestration of Prodigal, Eggnog-mapper, and TransTermHP, brings to light the coding regions, terminators, and functional classes of proteins.

Taxonomy Assignment

To assign taxonomy, PhageScope employ HMMs to align phage proteins against taxonomically representative VOGs. This meticulous taxonomic annotation ensures precise classification, an essential component in the intricate dance of genomic exploration.

Functional Annotation

Functional annotation, a crucial aspect of any genomic study, is where PhageScope truly shines. The tool employs tRNAscan-SE, ARAGORN, AcRanker, and CRISPRCasFinder, among others, to identify tRNA and tmRNA genes, anti-CRISPR proteins, and CRISPR arrays. The integration of mmseqs for homology searches against VFDB and CARD completes the picture, revealing virulence factors and antimicrobial resistance genes, if the matches meet stringent thresholds.

Comparative Genomics

The tool's prowess in comparative genomics is evident in its sequence clustering, sequence alignment, and comparative tree construction. Mmseqs takes center stage, generating subclusters and clusters with representative sequences. BLASTP performs pairwise alignments, showcasing coverage and identity values, while Alfpy and the neighbor-joining algorithm construct a comparative tree, unveiling hierarchies among multiple phages.

User Experience (The phage experience)

My hands-on exploration of PhageScope uncovered a user-friendly platform that marries functionality with aesthetics. The platform has a well designed page with easy to use functionality, having a range of tasks that a well sectioned. What I particularly appreciate about this tool is the availability of sample data, referred to by the developers as demo data. These datasets not only allow for visualization but also provide the option to execute, offering a practical insight into potential outcomes before processing one's own samples. The inclusion of demo data is a time-saving feature, enabling users to familiarize themselves with the tool and anticipate real results without the extended wait times associated with processing actual data. The shortened run time for samples further enhances the user experience, ensuring efficient exploration and understanding of the tool's capabilities.

PhageScope demo data and demo results
PhageScope demo data and demo results

An added advantage of the tool is that the developers have made it freely accessible without the need for user accounts. The work runs are automatically saved, and the results are easily accessible (downloadable), providing a seamless and user-friendly experience.

While the tool provides preset color contrasts and the option to view genomes in both linear and circular formats, certain limitations have become apparent. Specifically, the tool lacks fine controls for data manipulation. Additionally, the limited database led to inaccurate host predictions for certain phages associated with rare bacteria. Furthermore, intermittent delays suggested potential server strain during peak usage times.

PhageScope's Future

PhageScope is not just a tool; it's an expedition into the unexplored territories of bacteriophage genomics. As the scientific community eagerly anticipates updates and refinements, PhageScope remains poised to leave an indelible mark on the trajectory of phage biology and microbial ecology studies. The developers have done a very outstanding work on bringing this tool to life. I can surely recomend it for someone who has would like to use web based interface to annotate their phage. Also it can suite someone who want to get nice photos for their phage genomes. You can access PhageScope here. For more tools, please visit our tools section by clicking here


The cover image has been sourced from the original published study published by Ruo Han Wang, Shuo Yang, Zhixuan Liu, Yuanzheng Zhang, Xueying Wang, Zixin Xu, Jianping Wang, Shuai Cheng Li, PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations, Nucleic Acids Research, 2023;, gkad979,


AbbreviationFull FormExplanation for Layman
AcRankerAnti-CRISPR prediction toolA tool that predicts the presence of anti-CRISPR proteins, which can counteract CRISPR-based bacterial defenses.
AlfpyAlignment-Free Sequence Comparison MethodA method for comparing genetic sequences without aligning them, aiding in efficient analysis.
BLASTPBasic Local Alignment Search Tool for ProteinsA tool that searches for similar protein sequences in databases, helping identify proteins with shared features.
CARDComprehensive Antibiotic Resistance DatabaseA database that compiles information on antibiotic resistance genes, aiding in the study of drug resistance.
CheckVQuality Assessment Tool for Metagenome-Assembled GenomesA tool that assesses the quality of genomic data assembled from microbial communities.
CRISPRCasFinderCRISPR array detection toolA tool that identifies CRISPR arrays, which are part of a bacterial defense mechanism against viruses.
DDBJDNA Data Bank of JapanA database storing DNA sequences, serving as a valuable resource for genetic research.
DeepHostHost Prediction Tool using Deep LearningA tool that uses deep learning algorithms to predict the hosts (bacteria) that phages infect.
Eggnog-mapperEvolutionary Genealogy of Genes: Non-supervised Orthologous GroupsA tool that assigns evolutionary relationships to genes based on shared functions.
EMBLEuropean Molecular Biology LaboratoryA leading research institute supporting molecular biology studies and providing valuable data resources.
GPDGlobal Phage DatabaseA worldwide database collecting information on bacteriophages, viruses that infect bacteria.
GOV2Global Ocean Virome 2A global initiative studying viruses in the ocean, contributing to our understanding of marine ecosystems.
GVDGlobal Virome DatabaseA global database cataloging viral diversity, enhancing our knowledge of viruses and their impact.
IMG/VRIntegrated Microbial Genomes with Viral ResourcesA platform integrating microbial and viral genome data for comprehensive analysis.
IGVDIntegrated Global Viral DatabaseA global database consolidating viral information, facilitating research on global viral diversity.
MGVMetaGenomic Viral DatabaseA database focused on viruses identified through metagenomic studies, aiding in viral genome analysis.
PHROGPhage and Host Relations Ontology GraphA tool that helps researchers understand the relationships between bacteriophages and their host bacteria.
ProdigalProkaryotic Dynamic Programming Genefinding AlgorithmA tool that identifies genes in the DNA of bacteria, assisting in understanding bacterial genetic information.
RefSeqReference Sequence DatabaseA comprehensive database providing reference DNA sequences for various organisms, supporting genetic research.
STVSiphoviridae Viral DatabaseA database specializing in a family of bacteriophages called Siphoviridae, aiding research on these viruses.
TemPhDTemperate Phage DatabaseA database focused on temperate phages, which can integrate into bacterial DNA and remain dormant.
TMHMMTransmembrane Helix Prediction ToolA tool that predicts the presence of transmembrane helices in proteins, aiding in the study of protein structure.
TransTermHPTranscriptional Terminator Prediction for Bacterial GenomesA tool that predicts termination signals in bacterial DNA, assisting in understanding gene regulation.
tRNAscan-SEtRNA detection in genomesA tool that identifies transfer RNA (tRNA) genes in genomes, essential for protein synthesis.
VFDBVirulence Factor DatabaseA database containing information on virulence factors, which contribute to the severity of infections.
VOGViral Orthologous GroupsA system that groups together genes from different viruses that share evolutionary ancestry.
List of abbreviations used and their details

About the author

Hello there!

I'm Raphael Hans Lwesya. I have a deep interest in phage research and science communication. I strive to simplify complex ideas and present the latest phage-related research in an easy-to-digest format. Thank you for visiting The Phage blog. If you have any questions or suggestions, please feel free to leave a comment or contact me at [email protected].

Leave a Reply