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

Empirical codon substitution matrix.

Adrian Schneider1, Gina M Cannarozzi, Gaston H Gonnet

  • 1Institute of Computational Science, Swiss Federal Institute of Technology, Zurich, Switzerland. schneadr@inf.ethz.ch <schneadr@inf.ethz.ch>

BMC Bioinformatics
|June 2, 2005
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

Complex evolution of novel red floral color in Petunia.

The Plant cell·2021
Same author

Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters.

Microbiome·2019
Same author

First Release of the Bacterial Biobank of the Urban Environment (BBUE).

Microbiology resource announcements·2018
Same author

The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.

Nucleic acids research·2017
Same author

A Comparison of 2-Year Outcomes in Patients Undergoing Tibiofemoral or Patellofemoral Matrix-Induced Autologous Chondrocyte Implantation.

The American journal of sports medicine·2017
Same author

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference.

Bioinformatics (Oxford, England)·2017
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026
Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026
Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026
See all related articles

Researchers developed a novel empirical codon substitution matrix using vertebrate DNA, offering an alternative to traditional parameterized models for molecular evolution studies like Ka/Ks ratio calculation and ancestral DNA sequence reconstruction.

Area of Science:

  • Molecular Evolution
  • Genomics
  • Bioinformatics

Background:

  • Codon substitution probabilities are crucial for molecular evolution studies, including Ka/Ks ratio determination and ancestral DNA sequence reconstruction.
  • Historically, parameterized models were used, but increasing genomic data allows for empirical matrix construction.
  • This study introduces the first empirical codon substitution matrix derived entirely from vertebrate coding DNA sequences.

Purpose of the Study:

  • To present a new empirical codon substitution matrix based on vertebrate DNA.
  • To provide an alternative to existing parameterized models for codon evolution.
  • To facilitate accurate molecular evolution analyses.

Main Methods:

  • Utilized 17,502 alignments of orthologous sequences from five vertebrate genomes.

Related Experiment Videos

  • Analyzed 8.3 million aligned codons to count codon-to-codon substitutions.
  • Computed probability and similarity score matrices (64x64), focusing on sense codons (61x61).

    • Main Results:

    • Successfully constructed a comprehensive empirical codon substitution matrix from extensive vertebrate genomic data.
    • The matrix details substitution probabilities between all sense codons.
    • The study provides a valuable resource for molecular evolution research.

    Conclusions:

    • The availability of large genomic datasets enables the creation of empirical codon substitution matrices.
    • Further data is needed for specialized matrices (e.g., by kingdom or evolutionary distance).
    • Empirical matrices are advantageous for alignments at medium evolutionary distances and for applications like ancestral sequence reconstruction and Ka/Ks ratio calculation.