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

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.2K
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%...
18.2K
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

7.3K
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
7.3K
Point and Frameshift Mutations01:30

Point and Frameshift Mutations

306
Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
306
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

17.1K
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,...
17.1K
Genetic Screens02:46

Genetic Screens

5.2K
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
5.2K

You might also read

Related Articles

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

Sort by
Same author

Pseudomonads associated to salt-stressed plants facilitate stress adaption of soybean through enhanced lignin biosynthesis.

Science advances·2026
Same author

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures.

bioRxiv : the preprint server for biology·2026
Same author

An integrated single-nucleus ribonucleic acid sequencing and spatial transcriptomic atlas reveals stage-specific neuronal and glial trajectories in a mouse model of amyotrophic lateral sclerosis.

Neural regeneration research·2026
Same author

Surgical treatment for neonates with necrotising enterocolitis in the republic of Ireland: are we just seeing patients at the tip of the iceberg?

Irish journal of medical science·2026
Same author

Non-Wilms Renal Tumours in Children: The Republic of Ireland Experience.

Children (Basel, Switzerland)·2026
Same author

The power, potential of real-world data in randomized controlled trials: proceedings from a multistakeholder think tank.

Trials·2026
Same journal

Real-time Targeted Enrichment in Single-cell Long-read Sequencing.

Genomics, proteomics & bioinformatics·2026
Same journal

Decoding RNA N6-Methyladenosine Methylome of Wheat Using Machine Learning and Nanopore Direct RNA Sequencing.

Genomics, proteomics & bioinformatics·2026
Same journal

Tranquillyzer: A Neural Network Framework for Long-read Annotation and Demultiplexing.

Genomics, proteomics & bioinformatics·2026
Same journal

Advancing Functional Transcriptomics in Zebrafish with High-accuracy Full-length RNA Sequencing.

Genomics, proteomics & bioinformatics·2026
Same journal

NanoRAPID: A Deep Learning-based Framework for Single-molecule RNA Structure Analysis Using Nanopore Direct RNA Sequencing.

Genomics, proteomics & bioinformatics·2026
Same journal

Single-cell Multiomic and Spatiotemporal Dissection of the Liver Circadian Clock.

Genomics, proteomics & bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Oct 30, 2025

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

1.1K

Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants.

Jiadong Lin1, Xiaofei Yang2, Walter Kosters3

  • 1School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China; MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China; Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; Leiden Institute of Advanced Computer Science, Faculty of Science, Leiden University, Leiden 2311EZ, Netherland.

Genomics, Proteomics & Bioinformatics
|July 5, 2021
PubMed
Summary
This summary is machine-generated.

Mako, a novel tool, accurately detects complex structural variants (CSVs) using a model-free strategy. This advancement improves genomic alteration discovery by analyzing multi-breakpoint connections from short-read sequencing data.

Keywords:
Complex structural variantFormation mechanismGraph miningNext-generation sequencingPattern growth

More Related Videos

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

19.6K
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

13.2K

Related Experiment Videos

Last Updated: Oct 30, 2025

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

1.1K
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

19.6K
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

13.2K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Complex structural variants (CSVs) involve multiple breakpoints, making their detection challenging with current methods.
  • Limited progress has been made in discovering CSVs compared to simple structural variants due to detection complexities.

Purpose of the Study:

  • To develop a novel computational approach for detecting complex structural variants (CSVs) from paired-end short-read sequencing data.
  • To systematically analyze the multi-breakpoint connection features inherent to CSVs.

Main Methods:

  • Proposed Mako, a tool utilizing a bottom-up, guided, model-free strategy for CSV detection.
  • Implemented a graph-based pattern growth approach to identify potential breakpoint connections without pre-defined models.

Main Results:

  • Mako demonstrated superior performance over existing algorithms on simulated and real datasets.
  • Achieved approximately 70% validation rates for CSVs on real data, with median breakpoint shifts of 13 bp (experimental) and 26 bp (computational).
  • Identified 15 CSV types, including two novel types, and revealed the influence of sequence homology on CSV formation.

Conclusions:

  • Mako effectively detects and characterizes complex structural variants, advancing genomic alteration discovery.
  • The model-free, graph-based approach offers a robust strategy for identifying complex genomic rearrangements.
  • The study provides new insights into CSV types and their formation mechanisms.