Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Impact of timely vaccination and genomic surveillance on controlling consecutive waves of SARS-CoV-2 variants.

Scientific reports·2026
Same author

A Latin American perspective on microbiome research.

Nature communications·2025
Same author

Draft genome sequence of <i>Catenibacterium mistuoki</i> isolated from the fecal sample of a melanoma patient with complete response to immunotherapy.

Microbiology resource announcements·2025
Same author

Phages with a broad host range are common across ecosystems.

Nature microbiology·2025
Same author

Soil microbiome analysis of Uruguayan grasslands and croplands reveals losses of microbial diversity and necromass recycling traits.

Environmental microbiome·2025
Same author

Genetically divergent <i>Francisella philomiragia</i> associated with septic arthritis, Montevideo, Uruguay.

New microbes and new infections·2024

Related Experiment Video

Updated: Oct 17, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

9.4K

Protocol for post-processing of bacterial pangenome data using Pagoo pipeline.

Ignacio Ferrés1,2, Gregorio Iraola1,2,3,4

  • 1Microbial Genomics Laboratory, Institut Pasteur Montevideo, Montevideo, Montevideo 11400, Uruguay.

STAR Protocols
|October 11, 2021
PubMed
Summary

Interpreting bacterial pangenome data requires integrating genetic and phenotypic information. Pagoo is a new tool that standardizes this process, enabling flexible data analysis and storage for comparative studies.

Keywords:
BioinformaticsGenomicsMicrobiology

More Related Videos

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

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

Published on: December 7, 2021

2.5K
A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae
10:18

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

Published on: April 25, 2015

10.5K

Related Experiment Videos

Last Updated: Oct 17, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

9.4K
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

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

Published on: December 7, 2021

2.5K
A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae
10:18

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

Published on: April 25, 2015

10.5K

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Bacterial pangenome reconstruction software generates complex outputs requiring downstream analysis.
  • Current methods for integrating genetic and phenotypic data are user-dependent and lack standardization.

Purpose of the Study:

  • To introduce Pagoo, a novel post-processing tool for bacterial pangenome data.
  • To provide a standardized, flexible, and extensible framework for data integration, analysis, and storage.
  • To detail the protocol for running Pagoo and conducting comparative pangenome analyses.

Main Methods:

  • Development of Pagoo, a pangenome post-processing software.
  • Implementation of a standardized framework for data integration and analysis.
  • Protocol for running Pagoo on bacterial pangenome data.

Main Results:

  • Pagoo facilitates the integration of diverse genetic and phenotypic data.
  • The tool supports both simple and complex comparative analyses of bacterial pangenomes.
  • A standardized protocol for Pagoo usage is provided.

Conclusions:

  • Pagoo addresses the need for standardized downstream analysis of bacterial pangenome data.
  • The tool enhances data integration, analysis, and storage capabilities.
  • Pagoo enables more robust and reproducible comparative genomic studies.