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

Histone Variants at the Centromere02:30

Histone Variants at the Centromere

5.1K
Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
5.1K
Uncertainty in Measurement: Reading Instruments02:46

Uncertainty in Measurement: Reading Instruments

53.2K
Counting is the type of measurement that is free from uncertainty, provided the number of objects being counted does not change during the process. Such measurements result in exact numbers. By counting the eggs in a carton, for instance, one can determine exactly how many eggs are there in the carton. Similarly, the numbers of defined quantities are also exact. For example, 1 foot is exactly 12 inches, 1 inch is exactly 2.54 centimeters, and 1 gram is exactly 0.001 kilograms. Quantities...
53.2K
Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

7.6K
Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
7.6K
¹H NMR: Complex Splitting01:13

¹H NMR: Complex Splitting

1.9K
A proton M that is coupled to a proton X results in doublet signals for M. However, NMR-active nuclei can be simultaneously coupled to more than one nonequivalent nucleus. When M is coupled to a second proton A, such as in styrene oxide, each peak in the doublet is split into another doublet.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied...
1.9K
Structure of Lipids03:38

Structure of Lipids

99.1K
Lipids include a diverse group of compounds that are largely nonpolar in nature. This is because they are hydrocarbons that include mostly nonpolar carbon-carbon or carbon-hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), or insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic...
99.1K
Viral Structure00:56

Viral Structure

74.7K
Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.
74.7K

You might also read

Related Articles

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

Sort by
Same author

Mirrored structural symmetry index (VMSSI): a novel approach for diagnosing MR-negative focal cortical dysplasia using structural MRI.

Frontiers in neuroscience·2026
Same author

A mechanism-inspired integrated dual-frequency ultrasound transducer for cavitation-enhanced transdermal drug delivery.

Biomaterials·2026
Same author

Effect of chitosan and ε-Polylysine composite coating on postharvest quality maintenance and disease resistance of fresh <i>Tremella fuciformis</i>.

Food chemistry: X·2026
Same author

A novel glycolipid composite index predicting cardiovascular disease in Chinese adults with abnormal glucose metabolism: a nationwide cohort study.

Frontiers in cardiovascular medicine·2026
Same author

AND-logic amplification enables one-pot co-detection of extracellular vesicle miRNA and APE1.

Analytical biochemistry·2026
Same author

Giant Well-Differentiated Liposarcoma in the Retroperitoneal Space.

Journal of the College of Physicians and Surgeons--Pakistan : JCPSP·2026

Related Experiment Video

Updated: Feb 7, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

1.4K

Split-Read Indel and Structural Variant Calling Using PINDEL.

Kai Ye1,2,3,4, Li Guo5, Xiaofei Yang5

  • 1MOE Key Lab for Intelligent Networks & Network Security, Xi'an Jiaotong University, Xi'an, China. kaiye@xjtu.edu.cn.

Methods in Molecular Biology (Clifton, N.J.)
|July 25, 2018
PubMed
Summary
This summary is machine-generated.

This study details a protocol for detecting genetic variations like indels and structural variants using the Pindel algorithm. Accurate variant detection is key for understanding evolution, cell function, and diseases.

Keywords:
PINDELSplit-readStructural variants

More Related Videos

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.7K
Digital-Droplet PCR to Detect Indels Mutations in Genetically Modified Anopheline Mosquito Populations
05:51

Digital-Droplet PCR to Detect Indels Mutations in Genetically Modified Anopheline Mosquito Populations

Published on: June 28, 2021

4.0K

Related Experiment Videos

Last Updated: Feb 7, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

1.4K
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.7K
Digital-Droplet PCR to Detect Indels Mutations in Genetically Modified Anopheline Mosquito Populations
05:51

Digital-Droplet PCR to Detect Indels Mutations in Genetically Modified Anopheline Mosquito Populations

Published on: June 28, 2021

4.0K

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Genetic variations drive evolution and are crucial for understanding biological processes.
  • Accurate detection of genetic variants is essential for research into cell function, evolution, and diseases.
  • Short-read sequencing data is widely used for genomic analysis.

Purpose of the Study:

  • To describe a detailed protocol for discovering genetic variants.
  • To utilize the Pindel algorithm for variant detection.
  • To analyze Illumina short-read sequencing data.

Main Methods:

  • The study employs Pindel, a split-read algorithm.
  • The protocol is designed for processing Illumina short-read sequencing data.
  • The focus is on discovering insertions, deletions (indels), and structural variants.

Main Results:

  • A detailed protocol for indel and structural variant discovery is presented.
  • The Pindel algorithm is demonstrated as an effective tool for variant detection.
  • The protocol is applicable to biological samples generating short-read sequencing data.

Conclusions:

  • The Pindel algorithm provides an accurate and efficient method for detecting indels and structural variants.
  • This protocol facilitates a deeper understanding of genetic variations in various organisms.
  • The findings contribute to the advancement of genomic research and disease studies.