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

Next-generation Sequencing03:00

Next-generation Sequencing

99.9K
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....
99.9K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

21.2K
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.
21.2K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.9K
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...
4.9K
Sanger Sequencing01:57

Sanger Sequencing

776.5K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
776.5K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

19.1K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
19.1K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.9K
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%...
18.9K

You might also read

Related Articles

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

Sort by
Same author

Genome-scale evolution in local populations of wild chimpanzees.

Scientific reports·2025
Same author

Genome assembly of Genji firefly (Nipponoluciola cruciata) reveals novel luciferase-like luminescent proteins without peroxisome targeting signal.

DNA research : an international journal for rapid publication of reports on genes and genomes·2024
Same author

Arms race between anti-silencing and RdDM in noncoding regions of transposable elements.

EMBO reports·2023
Same author

A divergent RWP-RK transcription factor determines mating type in heterothallic Closterium.

The New phytologist·2022
Same author

Intraintestinal Analysis of the Functional Activity of Microbiomes and Its Application to the Common Marmoset Intestine.

mSystems·2022
Same author

Complete Genome Sequence of a Hyaluronate Lyase HysA- and HysB-Producing, Methicillin-Resistant Staphylococcus aureus Sequence Type 30, Staphylococcal Cassette Chromosome <i>mec</i> Type IVc Strain Isolated from Furunculosis in Japan.

Microbiology resource announcements·2022
Same journal

Analysis of strength degradation of coal and rock masses and stability of mined areas under long term immersion environment.

PloS one·2026
Same journal

Biogenic Silver-Selenium nanocomposite with anticancer activity and potent efficacy against vancomycin-resistant Staphylococcus aureus.

PloS one·2026
Same journal

Preparation and physicochemical characterization of a biodegradable chitosan/carboxymethyl cellulose hydrogel synthesized in NaOH/urea medium.

PloS one·2026
Same journal

Action-guilt, survivor-guilt, and depression in combat-related PTSD.

PloS one·2026
Same journal

Explainable machine learning for predicting activities of daily living at discharge in stroke patients: A retrospective study using SHAP interpretability.

PloS one·2026
Same journal

Deep learning based two-way feature depiction model for brain tumor detection.

PloS one·2026
See all related articles

Related Experiment Video

Updated: Mar 7, 2026

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

34.9K

DNApod: DNA polymorphism annotation database from next-generation sequence read archives.

Takako Mochizuki1, Yasuhiro Tanizawa1, Takatomo Fujisawa1

  • 1Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.

Plos One
|February 25, 2017
PubMed
Summary
This summary is machine-generated.

DNApod is a new database integrating plant DNA polymorphism data with uniform quality control. It provides analyzed data for rice, maize, and sorghum, enhancing data sharing and analysis for crops.

More Related Videos

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

38.1K
A Method to Study the C924T Polymorphism of the Thromboxane A2 Receptor Gene
07:00

A Method to Study the C924T Polymorphism of the Thromboxane A2 Receptor Gene

Published on: April 1, 2019

10.5K

Related Experiment Videos

Last Updated: Mar 7, 2026

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

34.9K
Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

38.1K
A Method to Study the C924T Polymorphism of the Thromboxane A2 Receptor Gene
07:00

A Method to Study the C924T Polymorphism of the Thromboxane A2 Receptor Gene

Published on: April 1, 2019

10.5K

Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • Next-generation sequencing (NGS) has generated vast DNA polymorphism datasets, but varying experimental and analytical conditions reduce reliability.
  • Current data distribution from individual projects hinders integrated access and consistent quality assessment.
  • A unified platform with uniform quality control is needed for reliable DNA polymorphism data integration.

Purpose of the Study:

  • To develop and present the DNA polymorphism annotation database (DNApod) for integrated, high-quality plant DNA polymorphism data.
  • To provide a single platform for accessing and analyzing genome-wide DNA polymorphism datasets under uniform conditions.
  • To facilitate knowledge sharing in plant genomics, particularly for crops.

Main Methods:

  • Integrated genome-wide DNA polymorphism datasets from re-analyzed whole-genome shotgun data.
  • Applied uniform analytical conditions, including raw data quality control, reference genome versions, and evaluation algorithms.
  • Developed DNApod as a centralized database with genome-wide DNA polymorphism data and known-gene annotations.

Main Results:

  • DNApod stores and distributes genome-wide DNA polymorphism datasets for 679 rice, 404 maize, and 66 sorghum strains.
  • The database ensures uniformity in data quality, reference genome, and analytical algorithms.
  • Provided links between genotypic and public phenotypic data, alongside tools for multiple alignment and phylogenetic tree construction.

Conclusions:

  • DNApod offers a reliable, integrated resource for plant DNA polymorphism data, prioritizing crops.
  • The database enhances data accessibility and comparability, supporting advanced genomic research.
  • Facilitates organism knowledge sharing through standardized analysis and cross-referencing with phenotypic data.