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Highly accurate prophage island detection with PIDE.

Hongyan Gao1,2, Bowen Li1,2, Zihan Guo1,2

  • 1Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing, 100084, China.

Genome Biology
|August 21, 2025
PubMed
Summary

We developed PIDE, a new tool to precisely identify prophages in bacterial genomes. This method uses a protein language model and clustering to find these mobile genetic elements, improving our understanding of bacterial populations.

Keywords:
Gene clusterHuman gut metagenomeProphage identificationProtein language model

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Prophages are mobile genetic elements crucial for prokaryotic evolution and bacterial population dynamics.
  • Accurate computational identification of prophages within host genomes remains a significant challenge.

Purpose of the Study:

  • To introduce PIDE, a novel computational tool for precise prophage identification in bacterial and metagenome-assembled genomes.
  • To enhance the study of prophage-host interactions and their impact on bacterial populations.

Main Methods:

  • PIDE integrates a pre-trained protein language model with a gene density clustering algorithm.
  • The tool was benchmarked using induced prophage sequencing datasets for validation.

Main Results:

  • PIDE accurately identifies prophages with precise genomic boundaries.
  • Analysis of 4,474 human gut representative genomes using PIDE revealed 24,467 prophages.
  • These identified prophages exhibit diverse and widespread functional capacities.

Conclusions:

  • PIDE offers a robust and precise method for prophage identification in diverse genomic contexts.
  • The tool facilitates large-scale analysis of prophage content and functional roles in bacterial communities.