Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Genome Annotation and Assembly

Genome Annotation and Assembly

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.

Multi-species Conserved Sequences

Multi-species Conserved Sequences

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...

Genetic Variation

Genetic Variation

Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

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%...

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

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...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

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...

You might also read

Related Articles

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

Sort by

Same author

DDX11-AS1 regulates cell cycle signaling pathway and promotes proliferation and migration of lung adenocarcinoma by sponging miR-30a-5p and targeting CCNA2.

Journal of applied genetics·2026

Same author

Fourier hybrid neural bathymetry network for active-passive fusion shallow water depth inversion.

Applied optics·2026

Same author

Two-Dimensional Dynamic Logic Resource Allocation for Scalable RIS Channel Emulation.

Sensors (Basel, Switzerland)·2026

Same author

Tumor suppressor genes and KRAS G12C inhibitor resistance in non-small cell lung cancer.

iScience·2026

Same author

ATACdb 2.0: a comprehensive chromatin accessibility database of human and mouse.

Nucleic acids research·2025

Same author

scVMAP: a comprehensive platform for integrating single-cell chromatin accessibility regions with causal variants.

Nucleic acids research·2025

Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026

Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026

Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026

Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026

Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026

Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Dec 4, 2025

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

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

Published on: August 15, 2019

VARAdb: a comprehensive variation annotation database for human.

Qi Pan¹, Yue-Juan Liu¹, Xue-Feng Bai¹

¹School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China.

Nucleic Acids Research

|October 23, 2020

Summary

This summary is machine-generated.

Researchers developed VARAdb, a human variation annotation database, to analyze non-coding variants. This resource integrates genetic and epigenomic data, aiding in understanding disease mechanisms and biological processes.

More Related Videos

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

Published on: August 20, 2019

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Published on: January 16, 2019

Related Experiment Videos

Last Updated: Dec 4, 2025

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

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

Published on: August 15, 2019

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

Published on: August 20, 2019

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Published on: January 16, 2019

Area of Science:

Genomics
Bioinformatics
Human Disease Research

Background:

Increasing identification of non-coding variants in human diseases.
Need for integrated genetic and epigenomic data to understand variant regulation.
Limitations of existing databases in specifically addressing non-coding variations.

Purpose of the Study:

To develop a comprehensive variation annotation database for human non-coding variants.
To provide a user-friendly platform for querying, browsing, and visualizing variant data.
To facilitate the interpretation of non-coding variants' effects on human diseases and biological processes.

Main Methods:

Development of VARAdb, a database integrating genetic and epigenomic data.
Inclusion of five annotation sections: Variation information, Regulatory information, Related genes, Chromatin accessibility, and Chromatin interaction.
Prioritization of variations using scores from nine annotation categories.

Main Results:

VARAdb contains annotation information for over 577 million variations, including novel variants.
Detailed annotation includes motif changes, risk SNPs, eQTLs, clinical variant-drug-gene pairs, and regulatory elements (enhancers, promoters).
The database supports pathway downstream analysis and visualization of variations.

Conclusions:

VARAdb is a valuable resource for researchers studying human diseases and biological processes.
It aids in selecting potentially functional variations and interpreting their impact.
The database enhances the understanding of non-coding variant roles in health and disease.