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

6.5K
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...
6.5K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.4K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.4K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

334
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
334
Conserved Binding Sites01:49

Conserved Binding Sites

4.7K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.7K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

13.5K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
13.5K
Next-generation Sequencing03:00

Next-generation Sequencing

95.3K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
95.3K

You might also read

Related Articles

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

Sort by
Same author

Sexual dimorphism of COVID-19 inspires drug repositioning and host-targeting immunotherapy for viral pneumonia.

Signal transduction and targeted therapy·2026
Same author

Genomic features associated with sustained mammalian transmission of avian influenza A viruses.

Nature microbiology·2026
Same author

Phylogenomics redefines the evolutionary history of mosquitoes.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

Broad neutralizing antibody response of a monomeric spike-based SARS-CoV-2 bivalent vaccine against diverse variants.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

Five-year longitudinal surveillance reveals the continual circulation of both alpha- and beta-coronaviruses in Plateau and Gansu pikas (<i>Ochotona</i> spp.) at Qinghai Lake, China<sup>1</sup>.

Emerging microbes & infections·2024
Same author

Erratum for Chan et al., "Tropism of and Innate Immune Responses to the Novel Human Betacoronavirus Lineage C Virus in Human <i>Ex Vivo</i> Respiratory Organ Cultures".

Journal of virology·2024

Related Experiment Video

Updated: Nov 6, 2025

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

2.9K

Alignment free sequence comparison methods and reservoir host prediction.

Bill Lee1, David K Smith1, Yi Guan1,2

  • 1State Key Laboratory of Emerging Infectious Diseases, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.

Bioinformatics (Oxford, England)
|May 8, 2021
PubMed
Summary
This summary is machine-generated.

Predicting virus reservoir hosts is crucial for managing infectious diseases. This study enhances machine learning models using genomic and digital signal processing data for more accurate host prediction, including for SARS-CoV-2.

More Related Videos

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
18:10

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Published on: June 16, 2011

29.8K
Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach
07:06

Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach

Published on: December 1, 2011

13.5K

Related Experiment Videos

Last Updated: Nov 6, 2025

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

2.9K
Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
18:10

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Published on: June 16, 2011

29.8K
Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach
07:06

Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach

Published on: December 1, 2011

13.5K

Area of Science:

  • Virology
  • Machine Learning
  • Bioinformatics

Background:

  • Identifying the reservoir host of emerging viruses like SARS-CoV-2 is critical for pandemic preparedness and managing infectious diseases.
  • Traditional methods for reservoir host identification include surveillance, experimental studies, and phylogenetics.
  • Machine learning (ML) offers a rapid approach to predict reservoir hosts using viral sequence data.

Purpose of the Study:

  • To enhance ML models for predicting virus reservoir hosts by integrating genomic traits, phylogenetic signatures, and digital signal processing (DSP)-based structural patterns.
  • To improve the accuracy of reservoir host prediction for known virus-host datasets and novel viruses, including SARS-CoV-2.
  • To develop a more uniform and accurate ML approach for reservoir host prediction.

Main Methods:

  • Extended a previous ML model combining sequence alignment and alignment-free methods with gradient boosting machines.
  • Incorporated DSP-based structural patterns into the ML model for a more uniform approach.
  • Applied the enhanced ML model to existing virus/reservoir host datasets and to SARS-CoV-2 and related viruses.

Main Results:

  • The enhanced ML model demonstrated improved prediction accuracy compared to previous methods.
  • The integration of genomic traits, phylogenetic neighborhood signatures, and DSP features led to better reservoir host predictions.
  • The model successfully predicted reservoir hosts for SARS-CoV-2 and related viruses.

Conclusions:

  • The developed ML approach, integrating genomic and structural patterns, significantly improves reservoir host prediction accuracy.
  • This method provides a valuable tool for identifying potential zoonotic threats and understanding virus origins.
  • The study contributes to the ongoing efforts in predicting and managing emerging infectious diseases.