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

In-phase implies large likelihood for independent codon model: distinguishing coding from non-coding sequences.

Wei-Mou Zheng1, Fang Wu

  • 1Institute of Theoretical Physics, Academia Sinica, PO Box 2735, Beijing 100080, People's Republic of China. zheng@itp.ac.cn

Journal of Theoretical Biology
|June 20, 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

Application of Physiologically-Based Pharmacokinetic Modeling to Predict Gastric pH-Dependent Drug-Drug Interactions for Weak Base Drugs.

CPT: pharmacometrics & systems pharmacology·2020
Same author

Plant transcriptome analysis reveals specific molecular interactions between alfalfa and its rhizobial symbionts below the species level.

BMC plant biology·2020
Same author

The effect of form of carboxymethyl-chitosan dressings on biological properties in wound healing.

Colloids and surfaces. B, Biointerfaces·2020
Same author

PGC-1α gene transfer restores adhesion and reendothelialization of endothelial progenitor cells from patients with hypertension.

Journal of human hypertension·2020
Same author

Prediction of generalization of ocular myasthenia gravis under immunosuppressive therapy in Northwest China.

BMC neurology·2020
Same author

In vitro effects of Triclocarban on adipogenesis in murine preadipocyte and human hepatocyte.

Journal of hazardous materials·2020
Same journal

Evolution of quantitative traits: exploring the ecological, social and genetic bases of adaptive polymorphism.

Journal of theoretical biology·2026
Same journal

The male-biased sex ratio in humans and its role in the transition from promiscuity to pair bonding.

Journal of theoretical biology·2026
Same journal

Quantifying the counter-intuitive effects of vaccination by coupling the transmission dynamics of COVID-19 and the evolution of human behaviors.

Journal of theoretical biology·2026
Same journal

An integrative model of FGF2-induced signaling and muscle cell proliferation.

Journal of theoretical biology·2026
Same journal

A hybrid reaction-diffusion and mechanical stimulus model for mandibular bone remodeling under chewing and vibratory loading.

Journal of theoretical biology·2026
Same journal

Integrated tick management strategies in fragmented peridomestic environments.

Journal of theoretical biology·2026
See all related articles

This study shows that DNA coding sequences have a higher likelihood in the correct reading frame. This finding allows for accurate frame discrimination using codon usage probabilities, validated in E. coli.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Determining the correct reading frame in DNA sequences is crucial for accurate gene identification and functional analysis.
  • The independent codon model provides a theoretical basis for understanding codon usage biases.
  • Previous methods often require complex models or extensive datasets for frame prediction.

Purpose of the Study:

  • To demonstrate that the correct DNA coding frame has a higher likelihood than incorrect frames under the independent codon model.
  • To establish that a single set of codon usage probabilities is sufficient for discriminating coding frames.
  • To validate the codon independency hypothesis and propose a self-learning approach for parameter estimation.

Main Methods:

  • Utilizing the independent codon model to analyze DNA coding sequences.

Related Experiment Videos

  • Employing mutual information and chi-squared analysis to assess codon independency.
  • Examining the Escherichia coli genome as a case study.
  • Developing a self-learning approach for training set generation.

    • Main Results:

    • The likelihood of a DNA coding sequence is asymptotically larger when read in the correct frame compared to incorrect frames.
    • Codon usage probabilities effectively discriminate between the correct and offset reading frames.
    • Analysis of the E. coli genome confirmed significant contrast between coding and offset frames, supporting codon independency.
    • The proposed self-learning method provides a viable strategy for estimating probability parameters.

    Conclusions:

    • The independent codon model accurately predicts the higher likelihood of the correct reading frame.
    • Codon usage probabilities are a robust feature for identifying the correct coding frame.
    • The findings have implications for gene prediction algorithms and genomic analysis, particularly in prokaryotes like E. coli.