PhageTerm

PhageTerm identifies bacteriophage DNA termini and determines their packaging mechanisms by analyzing next-generation sequencing (NGS) read count biases to locate packaging initiation and termination sites.

Key Features:

• Detection of DNA termini: Employs a theoretical and statistical framework to detect natural DNA termini by exploiting biases in NGS read counts at termini relative to other genomic regions, enabling precise localization of packaging start and end sites.
• Diverse packaging mechanism classification: Classifies known phage packaging mechanisms including 5'cos (Lambda), 3'cos (HK97), pac (P1), headful without a pac site (T4), DTR (T7), and host fragment (Mu).
• Validation on characterized phages: Has been validated using phages with well-characterized packaging mechanisms to assess reliability of termini and mechanism calls.
• Application to novel and public datasets: Has been applied to determine termini of nine Clostridium difficile phages and six additional phages sourced from the Sequence Read Archive.

Scientific Applications:

• Genome architecture analysis: Maps DNA termini and packaging patterns to inform structural and organizational studies of phage genomes.
• Phage-host interaction and evolution studies: Provides data on packaging strategies and termini diversity that can inform investigations of phage evolution and interactions with bacterial hosts.
• Phage therapy and antimicrobial research: Supplies termini and packaging information relevant to selecting and characterizing bacteriophages for applications against antibiotic-resistant bacteria.

Methodology:

Analyzes NGS read counts to detect termini-associated read count biases and applies a theoretical and statistical framework to identify natural DNA termini and classify packaging mechanisms.