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 Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.6K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.6K
Phylogenetic Trees03:21

Phylogenetic Trees

44.8K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
44.8K
Taxonomy01:31

Taxonomy

72.8K
Taxonomy is the science of defining and naming groups of biological organisms based on shared characteristics. It uses a hierarchy of increasingly inclusive categories with Latin names. The smallest units of taxonomy, species and genus, are used to assign a formal, taxonomic name to each species in a system. This classification system, referred to as binomial nomenclature, was formalized by Carolus Linnaeus in the 18th century.Hierarchy of TaxonomyThe hierarchy that Carolus Linnaeus first...
72.8K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.0K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
7.0K
Classification of Systems-II01:31

Classification of Systems-II

119
Continuous-time systems have continuous input and output signals, with time measured continuously. These systems are generally defined by differential or algebraic equations. For instance, in an RC circuit, the relationship between input and output voltage is expressed through a differential equation derived from Ohm's law and the capacitor relation,
119
Classification of Systems-I01:26

Classification of Systems-I

156
Linearity is a system property characterized by a direct input-output relationship, combining homogeneity and additivity.
Homogeneity dictates that if an input x(t) is multiplied by a constant c, the output y(t) is multiplied by the same constant. Mathematically, this is expressed as:
156

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

HybridGNN: a graph neural network approach for human miRNA-disease association prediction.

Bioinformatics (Oxford, England)·2026
Same author

RWRGDR: Random Walk and GraphSAGE-based Framework for Enhanced Drug Repositioning.

Current drug targets·2026
Same author

Unveiling the Therapeutic Mechanisms of Chinese Herbs in Heart Failure: Integrating Network Pharmacology, Molecular Docking, and Simulation Analysis.

Pharmaceuticals (Basel, Switzerland)·2025
Same author

tRNA is a molecular thermometer of species' optimal growth temperature.

International journal of biological macromolecules·2025
Same author

A protein pre-trained model-based approach for the identification of the liquid-liquid phase separation (LLPS) proteins.

International journal of biological macromolecules·2024
Same author

Investigating Potential Cancer Therapeutics: Insight into Histone Deacetylases (HDACs) Inhibitions.

Pharmaceuticals (Basel, Switzerland)·2024

Related Experiment Video

Updated: May 10, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

15.7K

Exploring species taxonomic kingdom using information entropy and nucleotide compositional features of coding

Sebu Aboma Temesgen1, Basharat Ahmad1, Bakanina Kissanga Grace-Mercure1

  • 1School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.

Methods (San Diego, Calif.)
|April 25, 2025
PubMed
Summary

This study analyzed DNA coding sequences across thousands of species using Markov processes. Results reveal distinct nucleotide preferences and evolutionary patterns, aiding in species classification and understanding genetic information flow.

Keywords:
Coding sequenceInformation entropyMachine learningNucleotide-compositionUMAP

More Related Videos

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.3K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.2K

Related Experiment Videos

Last Updated: May 10, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

15.7K
An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.3K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.2K

Area of Science:

  • Molecular Biology
  • Genomics
  • Evolutionary Biology

Background:

  • The central dogma describes DNA to protein information flow.
  • Genetic drift and mutations alter DNA composition, impacting protein-coding sequences (CDS).
  • Nucleotide distribution analysis in CDS is key to understanding species evolution.

Purpose of the Study:

  • To analyze codon formation and compositional changes in CDS across diverse species.
  • To explore evolutionary trends and species-specific nucleotide preferences.
  • To apply machine learning for species classification based on CDS evolution.

Main Methods:

  • Markov processes were applied to analyze codon formation in 37,031,061 CDSs from 3,735 species.
  • Information entropies and Markov information densities were calculated.
  • Uniform Manifold Approximation and Projection (UMAP) and machine learning were used for dimensionality reduction and classification.

Main Results:

  • Species-specific nucleotide preferences were identified.
  • Eukaryotes showed higher redundancy, while viruses exhibited high mutation rates.
  • Evolutionary trends indicated increasing information entropy and decreasing Markov entropy.
  • Machine learning models achieved high accuracy in species classification.

Conclusions:

  • The study provides insights into CDS evolution and protein synthesis across diverse taxa.
  • Nucleotide composition analysis reveals evolutionary adaptations and genomic strategies.
  • Machine learning effectively classifies species based on genomic sequence features.