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

6.8K
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...
6.8K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.5K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
18.5K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

20.4K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
20.4K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

15.2K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
15.2K
Genomics02:02

Genomics

39.5K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
39.5K
Next-generation Sequencing03:00

Next-generation Sequencing

97.5K
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....
97.5K

You might also read

Related Articles

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

Sort by
Same author

Positional identification of a candidate gene for MALE STERILITY 2 (MS2) by linkage mapping and transcriptomic data in Cryptomeria japonica D. Don.

BMC genomics·2026
Same author

Characterization of targeted knock-in achieved via tandem paired nicking mediated by CRISPR/Cas9 nickases.

Methods (San Diego, Calif.)·2025
Same author

A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don.

BMC genomics·2024
Same author

Efficient indexing and querying of annotations in a pangenome graph.

bioRxiv : the preprint server for biology·2024
Same author

Somatic mutation rates scale with time not growth rate in long-lived tropical trees.

eLife·2024
Same author

Odd-Paired is Involved in Morphological Divergence of Snail-Feeding Beetles.

Molecular biology and evolution·2024

Related Experiment Video

Updated: Jan 4, 2026

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

411.2K

Visualization tools for human structural variations identified by whole-genome sequencing.

Toshiyuki T Yokoyama1, Masahiro Kasahara2

  • 1Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.

Journal of Human Genetics
|November 1, 2019
PubMed
Summary

This review surveys over 30 structural variation (SV) visualization tools for human genomes. It categorizes SV visualization methods and details tool features to guide researchers in selecting appropriate software for their specific needs.

More Related Videos

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

10.3K
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

34.5K

Related Experiment Videos

Last Updated: Jan 4, 2026

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

411.2K
Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

10.3K
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

34.5K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Visualizing structural variations (SVs) is crucial for understanding their links to human traits and diseases.
  • Numerous sequencing platforms and diverse research objectives necessitate a variety of SV visualization tools.

Purpose of the Study:

  • To provide a comprehensive survey of over 30 SV visualization tools.
  • To assist researchers in selecting appropriate tools for visualizing SVs from human genome sequencing data.

Main Methods:

  • Categorization of SV visualization tools into ten distinct 'view modules'.
  • Detailed analysis of individual tools based on features like annotation integration, read alignment display, data structure, SV types, auditability, and platform compatibility.

Main Results:

  • Identification and categorization of over 30 existing SV visualization tools.
  • A systematic comparison of tools based on key visualization and data handling features.

Conclusions:

  • The survey categorizes SV visualization approaches and evaluates tool features to aid researchers.
  • This review aims to guide tool selection and stimulate the development of novel SV visualization solutions.