PhageScope

PhageScope annotates and classifies bacteriophage genomes infecting bacteria and archaea to provide comprehensive genomic annotations—covering genome completeness, host range, lifestyle, taxonomy, and structural and functional elements—to support studies of phage biology and applications such as phage therapy.

Key Features:

• Sequence collection: Contains 873,718 phage sequences.
• Annotation pipeline: Employs fifteen state-of-the-art tools to systematically annotate phage sequences.
• Genome completeness: Assesses the integrity and completeness of phage genomes.
• Host range prediction: Identifies potential host organisms for each phage, including bacteria and archaea.
• Lifestyle annotation: Provides information on phage lifestyle characteristics such as lytic and lysogenic cycles.
• Taxonomic classification: Offers detailed taxonomic classification for comparative and evolutionary analyses.
• Structural and functional element annotation: Annotates nine types of structural and functional genetic elements within phage genomes.
• Comparative genomics: Supports three types of comparative genomic studies.
• Automatic analysis and visualization: Integrates automatic analysis and visualization tools for annotated phage datasets.

Scientific Applications:

• Microbial ecosystem studies: Enables investigation of phage roles and diversity within microbial ecosystems.
• Phage therapy research: Supports identification and characterization of candidate therapeutic phages.
• Comparative genomics and evolution: Facilitates comparative studies and evolutionary analyses of phage lineages.
• Host–phage interaction studies: Informs analyses of host range and lifestyle relationships between phages and their bacterial or archaeal hosts.

Methodology:

PhageScope employs fifteen annotation tools to systematically process a collection of 873,718 phage sequences, producing assessments of genome completeness, host range, lifestyle, and taxonomic classification, annotating nine types of structural and functional genetic elements, supporting three types of comparative genomic studies, and integrating automatic analysis and visualization tools.