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

Annotation of bacterial genomes using improved phylogenomic profiles.

F Enault1, K Suhre, C Abergel

  • 1Structural and Genomic Information, CNRS-UPR 2589, 31 chemin Joseph Aiguier, 13009 Marseille, France. enault@igs.cnrs-mrs.fr

Bioinformatics (Oxford, England)
|July 12, 2003
PubMed
Summary
This summary is machine-generated.

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

Connecting the epigenome, metabolome and proteome for a deeper understanding of disease.

Journal of internal medicine·2021
Same author

Draft genome sequence of a novel Bacillus glycinifermentans strain having antifungal and antibacterial properties.

Journal of global antimicrobial resistance·2019
Same author

The Saliva Metabolome in Association to Oral Health Status.

Journal of dental research·2019
Same author

Complex Membrane Remodeling during Virion Assembly of the 30,000-Year-Old Mollivirus Sibericum.

Journal of virology·2019
Same author

Study of Cell Division Aberrations Induced by Some Silica Dusts in Mammalian Cells in Vitro.

Inhalation toxicology·2015
Same author

Non-truncating LIFR mutation: causal for prominent congenital pain insensitivity phenotype with progressive vertebral destruction?

Clinical genetics·2015

This study enhances phylogenomic profiling for inferring protein function by incorporating normalized scores and evolutionary distances. The improved method increases identified evolutionary relationships by 25% and provides reliable functional predictions with p-values.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Phylogenomic profiling infers protein function using evolutionary information.
  • The original method, described by Pellegrini et al. (1999), used a binary (absent/present) approach.
  • Existing methods lack reliability estimates for functional predictions.

Purpose of the Study:

  • To improve phylogenomic profiling for large-scale comparative genomics.
  • To enhance the accuracy and reliability of protein function inference.
  • To develop a method that avoids arbitrary cut-off values and provides statistical confidence.

Main Methods:

  • Utilized normalized Blastp bit scores and evolutionary distances for matrix normalization.
  • Defined a phylogenomic neighborhood based on continuous pairwise gene distances.

Related Experiment Videos

  • Developed an annotation procedure incorporating p-value computation for functional assignments.

    • Main Results:

    • Increased identification of evolutionarily related enzymes by approximately 25% compared to the binary method.
    • Achieved a false positive rate below 20%.
    • Demonstrated 50% accuracy in function attributions at a p-value threshold of 10(-11) on the MultiFun database.

    Conclusions:

    • The enhanced phylogenomic profiling method significantly improves the identification of evolutionary relationships and protein function.
    • The approach provides reliable functional predictions with associated p-values, applicable to new microbial genomes.
    • This method offers a robust alternative to existing techniques by avoiding arbitrary cut-offs and quantifying prediction reliability.