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

A nucleotide substitution model with nearest-neighbour interactions.

Gerton Lunter1, Jotun Hein

  • 1Bioinformatics group, Department of Statistics, University of Oxford, Oxford, UK. lunter@stats.ox.ac.uk

Bioinformatics (Oxford, England)
|July 21, 2004
PubMed
Summary

Neighboring DNA nucleotides influence mutation rates. Our new context-dependent substitution model reveals significant neighbor dependencies, like increased CpG to TpG/CpA rates, aiding evolutionary analysis.

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

Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder.

... International Conference on Learning Representations·2026
Same author

Cardiovascular-kidney-metabolic syndrome: candidate subtypes and genetic risk factors.

BMC medical genomics·2026
Same author

Lifestyle Patterns and Incidence of Cardiovascular Diseases, Cancer, Respiratory Diseases, and Type 2 Diabetes: A Large-Scale Prospective Cohort Study.

Nutrients·2025
Same author

A genome- and phenome-wide association study of plasma procalcitonin concentrations in individuals of European ancestry.

EBioMedicine·2025
Same author

Protocol for using treeLFA to infer multimorbidity patterns in the form of disease topics from diagnosis data in biobanks.

STAR protocols·2025
Same author

Propofol-based versus sevoflurane-based anaesthesia for deceased donor kidney transplantation: the VAPOR-2 study protocol for an international multicentre randomised controlled trial.

BMJ open·2025

Area of Science:

  • Evolutionary biology
  • Genomics
  • Bioinformatics

Background:

  • Nucleotide mutations are not independent events.
  • Understanding context-dependent mutation is crucial for evolutionary studies.

Purpose of the Study:

  • Introduce a context-dependent substitution model for DNA evolution.
  • Develop an algorithm to calculate sequence evolution likelihood under this model.
  • Estimate neighbor-dependent and dinucleotide substitution rates.

Main Methods:

  • Developed a context-dependent substitution model.
  • Derived an algorithm for likelihood calculation.
  • Employed Bayesian sampling for rate estimation.
  • Applied the model to human-mouse non-coding DNA.

Related Experiment Videos

Main Results:

  • Observed clear neighbor dependencies in DNA substitution rates.
  • Identified 17-18 fold increased CpG to TpG/CpA rates.
  • Inferred root position between human and mouse sequences, suggesting clock-like evolution.

Conclusions:

  • The context-dependent model accurately captures mutation patterns.
  • Neighbor dependencies, especially CpG mutations, significantly impact DNA evolution.
  • The irreversible model allows root inference without out-groups, supporting evolutionary rate studies.