PhageFinder

PhageFinder identifies and classifies prophage regions in completed bacterial genomes to enable detection and characterization of prophages.

Key Features:

• Prophage identification: Identifies prophage regions within completed bacterial genomes.
• Classification: Classifies identified prophage regions.
• Algorithmic approach: Implemented as a heuristic computer program.
• Performance: Evaluated on 42 bacterial genomes with manually identified prophages, detecting 91% of prophage regions with 7% false positives and 9% false negatives.
• Large-scale screening: Applied to 302 complete bacterial genomes, predicting 403 putative prophage regions comprising approximately 2.7% of the analyzed bacterial DNA.
• Integration site analysis: Analyzed 285 putative attachment sites and reported target distributions of tRNAs (33%), intergenic regions (31%), intragenic regions (28%), and tmRNAs (8%).
• Targeted tRNAs: Most commonly targeted tRNAs include Arginine (Arg), Leucine (Leu), Serine (Ser), and Threonine (Thr).
• Insertion point mapping: Mapped novel insertion points on the 5' side of the D loop, the 3' side of the anticodon loop, and within the anticodon.
• Phylogenetic analysis: Constructs phylogenetic trees based on the mean of the BLAST score ratio (BSR) of phage/prophage proteomes.

Scientific Applications:

• Prophage detection: Detection and classification of prophage regions in completed bacterial genomes.
• Genome-scale surveys: Prediction and cataloging of putative prophage regions across large sets of complete bacterial genomes.
• Integration site profiling: Mapping and statistical characterization of prophage attachment sites, including tRNAs and tmRNAs.
• Phylogenetic characterization: Reconstruction of phage/prophage relationships using mean BSR-based phylogenetic trees to verify bacteriophage groups.
• Prophage relationship analysis: Comparative analysis of prophage proteomes to inform understanding of prophage groupings and relationships.

Methodology:

Implemented as a heuristic computer program and constructs phylogenetic trees using the mean BLAST score ratio (BSR) of phage/prophage proteomes.