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

Accounting for background nucleotide composition when measuring codon usage bias: brilliant idea, difficult in

Anders Fuglsang

    Molecular Biology and Evolution
    |May 9, 2006
    PubMed
    Summary

    The effective number of codons (Nc) measures gene codon usage but ignores background nucleotide composition. A corrected variant, Nc

    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

    Conformational dynamics of CRISPR-Cas type I-F-HNH inform nickase engineering in a cascade scaffold.

    Nucleic acids research·2026
    Same author

    Evaluation of Incurred Subject Period Re-analysis (ISPR) as a Tool to Distinguish Fraudulent Pharmacokinetic Profile Pairs from Non-fraudulent Pairs.

    The AAPS journal·2024
    Same author

    Conformational landscape of the type V-K CRISPR-associated transposon integration assembly.

    Molecular cell·2024
    Same author

    Retron-Eco1 assembles NAD<sup>+</sup>-hydrolyzing filaments that provide immunity against bacteriophages.

    Molecular cell·2024
    Same author

    Structure of the TnsB transposase-DNA complex of type V-K CRISPR-associated transposon.

    Nature communications·2022
    Same author

    Increased Patient's Risk Associated with the Canadian Bioequivalence Guidance Due to Outlier Removal.

    Therapeutic innovation & regulatory science·2021

    Area of Science:

    • Genomics
    • Bioinformatics
    • Molecular Biology

    Background:

    • The effective number of codons (Nc) is a standard metric for quantifying codon usage bias in genes.
    • Traditional Nc analysis does not account for background nucleotide composition, potentially skewing results.
    • Novembre's Nc' variant was proposed to correct for background nucleotide composition in codon usage bias analysis.

    Discussion:

    • This study critically examines the properties of the Nc' estimator, focusing on codon homozygosity.
    • A theoretical inaccuracy in the Nc estimator is detailed: it ranges from 0 to 61, not 20 to 61.
    • Empirical data from the Pseudomonas aeruginosa genome illustrate the practical implications of this theoretical misunderstanding.

    Key Insights:

    • The Nc' estimator provides a more accurate measure of codon usage bias by incorporating background nucleotide composition.

    Related Experiment Videos

  • A common misconception regarding the Nc estimator's range (0-61 vs. 20-61) is clarified.
  • Real-world genomic data confirms the theoretical issues with standard Nc calculations.

    • Outlook:

    • Refined understanding of codon usage bias metrics is crucial for accurate comparative genomics.
    • Further research may explore the impact of background composition on other genetic measures.
    • This work encourages re-evaluation of existing codon usage bias studies that did not account for nucleotide composition.