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 Experiment Videos

Automatic selection of representative proteins for bacterial phylogeny.

Marshall Bern1, David Goldberg

  • 1Palo Alto Research Center, 3333 Coyote Hill Road, Palo Alto, CA 94304, USA. bern@parc.com

BMC Evolutionary Biology
|June 2, 2005
PubMed
Summary

This study introduces an algorithm to automatically select reliable protein families for bacterial phylogeny, overcoming issues like horizontal gene transfer. The method generates a robust phylogenetic tree, supporting key bacterial clades.

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

Lifetime management of aortic stenosis: A primer for the generalist.

The American journal of medicine·2026
Same author

Refining the definition of ACLF - keeping score and changing the game.

Journal of hepatology·2026
Same author

Comparative Prognostic Accuracy of Model for End-Stage Liver Disease Scores and the Freiburg Index of Post-Transjugular Intrahepatic Portosystemic Shunt Survival in Patients Undergoing Transjugular Intrahepatic Portosystemic Shunt Procedure for Ascites or Gastroesophageal Bleeding: A Meta-Analysis of Time-Specific Mortality.

Journal of vascular and interventional radiology : JVIR·2026
Same author

Differential survival benefit of curative versus non-curative intent treatment in a real-world cohort with early and intermediate-stage hepatocellular carcinoma.

Hepatology communications·2026
Same author

Spatial accessibility ratio: Will it improve access for liver transplantation?

Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society·2026
Same author

State-Level Variability in Location of Death of Patients with End-Stage Liver Disease.

Digestive diseases and sciences·2025

Area of Science:

  • Microbiology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Deep bacterial phylogeny is challenging due to horizontal gene transfer and phylogenetic noise.
  • Previous methods relied on manual curation, yielding inconsistent phylogenies with low confidence.
  • Approximately 200 complete bacterial genomes are available, necessitating improved phylogenetic analysis.

Purpose of the Study:

  • To develop an automated algorithm for selecting reliable protein families for bacterial phylogenetic analysis.
  • To construct a robust and well-resolved phylogenetic tree for diverse bacterial species.
  • To address the limitations of manual curation in phylogenetic character selection.

Main Methods:

  • An algorithm was developed to automatically identify "representative" protein families from complete bacterial genomes.

Related Experiment Videos

  • Representative protein families were selected based on their agreement with organismal distance matrices derived from conserved proteins.
  • Maximum-likelihood methods were used to compute phylogenetic trees from concatenated representative protein sequences.

    • Main Results:

    • The algorithm successfully identified representative protein families, enabling robust phylogenetic character selection.
    • Phylogenetic trees computed using representative proteins showed good agreement with manually curated methods.
    • The study validated the methodology on known phylogenetic questions and produced a well-resolved tree for diverse bacteria.
    • The resulting tree supports proposed high-level bacterial clades, including "Terrabacteria" and a clade containing Planctomycetes and Chlamydiales.

    Conclusions:

    • Automatically selected representative proteins offer an effective solution for phylogenetic character selection in bacteria.
    • This automated approach enhances the reliability and resolution of deep bacterial phylogenies.
    • The findings contribute to a more accurate understanding of bacterial evolutionary relationships.