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

Bootstrap confidence levels for HIV-1 recombination.

Karin S Dorman1, Andrew H Kaplan, Janet S Sinsheimer

  • 1Department of Biomathematics, University of California at Los Angeles, 90095, USA.

Journal of Molecular Evolution
|February 1, 2002
PubMed
Summary

This study introduces a novel bias-corrected accelerated percentile interval (BCa) bootstrap method to assess confidence in human immunodeficiency virus type 1 (HIV-1) recombination. This approach offers a more accurate, single overall confidence measure compared to traditional segment-by-segment methods.

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

p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation.

Nature communications·2024
Same author

The Undiagnosed Diseases Network: Characteristics of solvable applicants and diagnostic suggestions for nonaccepted ones.

Genetics in medicine : official journal of the American College of Medical Genetics·2024
Same author

Dynamic relationships among pathways producing hydrocarbons and fatty acids of maize silk cuticular waxes.

Plant physiology·2024
Same author

Nod1-dependent NF-kB activation initiates hematopoietic stem cell specification in response to small Rho GTPases.

Nature communications·2023
Same author

Patterns of reproduction and autozygosity distinguish the breeding from nonbreeding gray wolves of Yellowstone National Park.

The Journal of heredity·2023
Same author

An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species.

PloS one·2023

Area of Science:

  • * Evolutionary Biology
  • * Virology
  • * Bioinformatics

Background:

  • * Human immunodeficiency virus type 1 (HIV-1) genomes exhibit complex evolutionary relationships attributed to recombination.
  • * Traditional methods for confirming HIV-1 recombination rely on segment-by-segment nonparametric bootstrap analysis.
  • * These segment-based approaches can be labor-intensive and may not provide a unified measure of confidence.

Purpose of the Study:

  • * To develop and present a new, more accurate method for assessing confidence in HIV-1 recombination.
  • * To offer a single, overall confidence measure for HIV-1 recombinant data, improving upon existing techniques.
  • * To provide a robust alternative to the commonly used segment-by-segment nonparametric bootstrap.

Main Methods:

Related Experiment Videos

  • * Application of the bias-corrected accelerated percentile interval (BCa) bootstrap method.
  • * Extension of the BCa method previously used for inferring evolutionary relationships.
  • * Adaptation of the BCa method to address the "problem of regions" in sequence analysis.

    • Main Results:

    • * The new BCa bootstrap method provides a single, overall confidence measure for HIV-1 recombination.
    • * This method demonstrates higher accuracy compared to traditional segment-by-segment bootstrap procedures.
    • * The method was successfully tested on a dataset of 61 HIV-1 sequences, including 16 with uncertain recombinant status.

    Conclusions:

    • * The BCa bootstrap method offers a more accurate and efficient approach to assessing HIV-1 recombination confidence.
    • * This novel technique simplifies the interpretation of recombinant data by providing a unified confidence metric.
    • * The findings suggest a significant advancement in the analysis of viral evolution and genetic diversity.