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Related Experiment Video

Updated: Dec 23, 2025

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
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Phigaro: high-throughput prophage sequence annotation.

Elizaveta V Starikova1, Polina O Tikhonova1, Nikita A Prianichnikov1

  • 1Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow 119435, Russia.

Bioinformatics (Oxford, England)
|April 21, 2020
PubMed
Summary

Phigaro is a new tool that identifies prophage regions in genomes and metagenomes. This command-line application also visualizes prophage maps and potential transposon sites.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Microbial Ecology

Background:

  • Prophages, the integrated forms of bacteriophage genomes within bacterial hosts, play crucial roles in microbial evolution and community dynamics.
  • Accurate identification of prophage regions is essential for understanding their impact on host genomes and ecological functions.
  • Current methods for prophage detection can be limited in scope, particularly when dealing with complex metagenomic data.

Purpose of the Study:

  • To develop a robust and efficient tool for the detection and characterization of prophage regions in both individual genomes and complex metagenomic datasets.
  • To provide a user-friendly command-line application for researchers to mine and analyze prophage sequences.
  • To generate dynamic, annotated prophage genome maps for better visualization and analysis of prophage elements.

Main Methods:

  • Phigaro is a standalone command-line application developed in Python.
  • The tool accepts raw genome and metagenome assemblies as input for prophage detection.
  • It incorporates algorithms to identify prophage sequences and predict potential transposon insertion sites within these regions.

Main Results:

  • Phigaro successfully detects prophage regions from various genomic and metagenomic assemblies.
  • The application generates dynamic, annotated prophage genome maps, aiding in visualization and interpretation.
  • It accurately identifies potential transposon insertion sites within detected prophage regions.

Conclusions:

  • Phigaro offers a powerful and versatile solution for prophage region mining, especially from large metagenomic datasets.
  • The tool enhances the study of prophages by providing detailed genomic maps and insertion site information.
  • Phigaro is freely available, promoting accessibility and further research in prophage biology and metagenomics.