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Related Experiment Video

Updated: Jun 29, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes.

Conner J Copeland¹, Jack W Roddy², Amelia K Schmidt¹

¹Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.

NAR Genomics and Bioinformatics

|April 8, 2024

Summary

This summary is machine-generated.

VIBES automates prophage annotation in bacterial genomes, aiding the study of viral integrations and their impact on bacterial fitness and virulence. This tool enhances our understanding of bacteriophages and their roles in microbial ecosystems.

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Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

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Last Updated: Jun 29, 2025

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Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

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Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Published on: May 26, 2013

Area of Science:

Microbiology
Bioinformatics
Genomics

Background:

Bacteriophages, viruses infecting bacteria, can integrate into host genomes as prophages.
Prophages influence bacterial fitness, acting as parasites or mutualists, and can affect host virulence.
Advancements in bacterial genome sequencing enable detailed exploration of prophage prevalence and insertion sites.

Purpose of the Study:

To introduce VIBES (Viral Integrations in Bacterial genomES), a workflow for automated prophage annotation in bacterial genomes.
To provide context for prophage annotations by including bacterial gene and viral protein annotation.
To offer a versatile tool for general-purpose sequence similarity searches.

Main Methods:

VIBES is a Nextflow-driven workflow for automated prophage annotation.
It utilizes containerization for software dependencies, ensuring consistent execution across computing environments.
The workflow performs alignment-based searches and generates visualizations for data exploration.

Main Results:

VIBES successfully automates prophage annotation in complete bacterial genomes.
The workflow was demonstrated by searching 178 Pf phage genomes across 1072 *Pseudomonas* spp. genomes.
VIBES provides results in a tab-separated format with interactive visualizations.

Conclusions:

VIBES is an efficient and user-friendly tool for prophage annotation.
The workflow facilitates the study of prophage-host interactions and their evolutionary implications.
VIBES's design supports broader applications in sequence similarity searching.