ProphET

ProphET predicts prophage sequences in bacterial genomes to identify integrated phage regions and enable analysis of their impacts on host gene content and evolution.

Key Features:

• Self-Updating Reference Database: Utilizes a self-updating database of prophage genes for similarity-based detection.
• Input Formats: Operates on bacterial genome sequences in FASTA format with corresponding gene annotations in GFF format.
• Detection Strategy: Detects prophage regions by similarity searches against the prophage gene database and by assessing local prophage gene density.
• Performance Evaluation: Demonstrated high precision and scalability in benchmarking on 54 bacterial genomes containing 267 manually annotated prophages.

Scientific Applications:

• Prokaryotic Evolution Studies: Enables analysis of phage-mediated gene transfer, gene inactivation, and modulation of gene expression in bacterial genomes.
• Phage Therapy and Resistance Research: Facilitates cataloging of prophages relevant to virulence and antibiotic resistance and supports investigations related to phage therapy.

Methodology:

Performs similarity searches of input FASTA genomes and GFF annotations against its prophage gene database, calculates prophage gene density within candidate regions, and refines predicted region boundaries (edge refinement).