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

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.0K
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...
4.0K
RNA-seq03:21

RNA-seq

10.1K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.1K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

52
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...
52
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

10.9K
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...
10.9K

You might also read

Related Articles

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

Sort by
Same author

CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individuals.

bioRxiv : the preprint server for biology·2026
Same author

Defining a tandem repeat catalog and variation clusters for genome-wide analyses and population databases.

American journal of human genetics·2026
Same author

A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes.

bioRxiv : the preprint server for biology·2026
Same author

Author Correction: Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes.

Nature genetics·2026
Same author

Dual-targeting nuclear and mitochondrial DNA damage drives immunogenic activation via PANoptosis for synergistic magneto-thermodynamic-chemotherapy.

Biomaterials·2025
Same author

Long-read sequencing identifies FGF14 repeat expansions in Parkinson's disease.

Brain : a journal of neurology·2025
Same journal

Somatic mobility of transposons is explosive and shaped by distinct integration biases in Arabidopsis thaliana.

Genome biology·2026
Same journal

UK Biobank whole-genome sequencing reveals robust contributions of rare variants to complex-trait heritability.

Genome biology·2026
Same journal

A one-week automated genome-wide optical pooled screen using OttoSeq.

Genome biology·2026
Same journal

Integrated lipidomic and transcriptomic profiling of the host response in human malaria.

Genome biology·2026
Same journal

Centromeric satellite expansion drives genome evolution in the snowy owl.

Genome biology·2026
Same journal

Mapping the landscape of allele-specific expression in porcine genomes.

Genome biology·2026
See all related articles

Related Experiment Video

Updated: Jul 21, 2025

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

10.5K

vamos: variable-number tandem repeats annotation using efficient motif sets.

Jingwen Ren1, Bida Gu1, Mark J P Chaisson2

  • 1Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, US.

Genome Biology
|July 27, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces vamos, a new method for analyzing variable-number tandem repeats (VNTRs) in the human genome. vamos captures VNTR diversity more effectively than current methods, revealing significantly more alleles per locus.

Keywords:
Long-read sequencingMotif compositionVariable-number tandem repeats

More Related Videos

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

9.3K
Multi-locus Variable-number Tandem-repeat Analysis of the Fish-pathogenic Bacterium Yersinia ruckeri by Multiplex PCR and Capillary Electrophoresis
10:33

Multi-locus Variable-number Tandem-repeat Analysis of the Fish-pathogenic Bacterium Yersinia ruckeri by Multiplex PCR and Capillary Electrophoresis

Published on: June 17, 2019

10.9K

Related Experiment Videos

Last Updated: Jul 21, 2025

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

10.5K
Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

9.3K
Multi-locus Variable-number Tandem-repeat Analysis of the Fish-pathogenic Bacterium Yersinia ruckeri by Multiplex PCR and Capillary Electrophoresis
10:33

Multi-locus Variable-number Tandem-repeat Analysis of the Fish-pathogenic Bacterium Yersinia ruckeri by Multiplex PCR and Capillary Electrophoresis

Published on: June 17, 2019

10.9K

Area of Science:

  • Genomics
  • Bioinformatics
  • Population Genetics

Background:

  • Variable-number tandem repeats (VNTRs) constitute approximately 3% of the human genome.
  • VNTR loci are highly polymorphic, crucial for genetic studies.
  • Existing methods for VNTR variant analysis, based on alignment breakpoints, often underestimate their true diversity.

Purpose of the Study:

  • To develop a novel computational method for comprehensively annotating VNTRs.
  • To improve the characterization of VNTR allelic diversity in the human genome.
  • To overcome limitations of breakpoint-based VNTR analysis.

Main Methods:

  • Introduction of vamos (VNTR Annotation using efficient Motif Sets).
  • Annotation of VNTRs based on repeat composition and varying motif diversity levels.
  • Application of vamos to 74 haplotype-resolved human genome assemblies.

Main Results:

  • vamos estimates a higher number of alleles per VNTR locus compared to traditional methods.
  • Analysis revealed an estimated 7.4-16.7 alleles per locus using vamos.
  • Breakpoint-based approaches estimated only 4.0-5.5 alleles per locus.

Conclusions:

  • vamos provides a more accurate and comprehensive assessment of VNTR allelic diversity.
  • The method enhances our understanding of genomic variation at VNTR loci.
  • vamos offers a significant advancement for genomic and population genetics research.