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

Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location

François Enault1, Karsten Suhre, Olivier Poirot

  • 1Information Génomique & Structurale (UPR CNRS 2589), Institut de Biologie Structurale et Microbiologie, 31, chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. enault@igs.cnrs-mrs.fr

Nucleic Acids Research
|June 25, 2004
PubMed
Summary

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

Professional Academies: The Duty to Lead.

Microbial biotechnology·2026
Same author

Infection cycles of viruses of the phylum Nucleocytoviricota.

Nature reviews. Microbiology·2026
Same author

The 4.4 Å Capsid Structure of the Giant Melbournevirus Belonging to the <i>Marseilleviridae</i> Family.

Viruses·2026
Same author

Elucidating the protein interaction network of one of the largest icosahedral capsids in the virosphere.

The EMBO journal·2026
Same author

Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life.

Cell·2026
Same author

Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life.

bioRxiv : the preprint server for biology·2025

Phydbac2 enhances phylogenomic profiling for bacterial genes by integrating chromosomal proximity and gene fusion, improving functional prediction accuracy by 27% with a larger genome database.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Phylogenomic profiling aids in predicting gene function.
  • The original Phydbac tool used normalized BLAST scores for phylogenomic profiling.
  • Predictive power was limited compared to classical methods.

Purpose of the Study:

  • To present Phydbac2, a major extension of the Phydbac web service.
  • To enhance the prediction of pairwise gene functional relationships.
  • To expand the scope of phylogenomic profiling with new indicators and a larger genome dataset.

Main Methods:

  • Integrated chromosomal proximity and gene fusion analyses.
  • Expanded the reference genome set to 150 bacterial and eukaryotic genomes.
  • Utilized KEGG metabolic pathway database for benchmarking predictive power.

Related Experiment Videos

Main Results:

  • Achieved a 27% improvement in predictive power over the previous version.
  • Increased number of reference genomes contributed 11% to the gain.
  • Inclusion of chromosomal proximity in distance measure accounted for 16% improvement.

Conclusions:

  • Phydbac2 significantly improves the accuracy of gene function prediction.
  • The expanded functionality supports analysis of diverse bacterial groups, pathogens, and bio-terrorism agents.
  • New features facilitate comparative genomics and functional inference.