DEPhT

DEPhT identifies, extracts, and annotates complete phage and prophage sequences within bacterial genomes to enable analysis of prophage prevalence, distribution, and their roles in bacterial metabolism, pathogenicity, antibiotic resistance, and defense mechanisms.

Key Features:

• Multimodal run modes: Three run modes for rapid screening of large-scale bacterial genome datasets, precise extraction of prophage sequences, and comprehensive annotation of extracted prophages.
• Genomic architectural discrimination: Utilizes genomic architectural features to differentiate phage and bacterial sequences and improve prophage discovery accuracy.
• Targeted homology searches: Employs targeted homology searches to precisely extract complete prophage elements from complex bacterial genomes.
• Adaptability across bacterial genomes: Methodology developed for Mycobacterium genomes and broadly adaptable to other bacterial species for comparative genomic studies.
• Speed and sensitivity: Enables fast and sensitive discovery, extraction, and annotation of complete phage and prophage sequences in bacterial genomes.

Scientific Applications:

• Prophage prevalence and distribution: Demonstrates prophage prevalence across various Mycobacterium strains and absence from well-characterized Mycobacterium tuberculosis strains and approximately 30,000 sequenced M. tuberculosis genomes.
• Evolutionary dynamics: Enables study of phage–bacteria evolutionary dynamics and their impacts on bacterial pathogenicity, metabolism, antibiotic resistance, and defense mechanisms.
• Comparative genomics and functional studies: Supports comparative genomics and functional analyses by extracting and annotating complete prophage elements for downstream study.

Methodology:

Integrates analysis of genomic architectural features and targeted homology searches and operates in three run modes for rapid screening, prophage extraction, and annotation.