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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

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%...
Next-generation Sequencing03:00

Next-generation Sequencing

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.
Genetic Variation01:25

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, which...
Evolutionary Relationships through Genome Comparisons02:54

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...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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,...
Sanger Sequencing01:57

Sanger Sequencing

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...

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Related Experiment Video

Updated: May 18, 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

VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data.

Mark D Preston1, Magnus Manske, Neil Horner

  • 1Faculties of Epidemiology & Population Health and Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.

Bioinformatics (Oxford, England)
|September 15, 2012
PubMed
Summary

A new software, VarB, enables real-time analysis and visualization of genetic variations, including single-nucleotide polymorphisms and structural variants. This tool aids in identifying genomic regions under selection and differentiating populations, as demonstrated with Plasmodium falciparum data.

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Last Updated: May 18, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Published on: April 4, 2018

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Published on: February 24, 2015

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Area of Science:

  • Genomics
  • Bioinformatics
  • Parasitology

Background:

  • Advancements in sequencing technologies necessitate new tools for analyzing complex genetic data.
  • Identifying genetic variations like single-nucleotide polymorphisms (SNPs), insertions, and deletions is crucial for understanding disease.
  • Structural variants play a significant role in evolutionary adaptation and drug resistance.

Purpose of the Study:

  • To develop and present VarB, a novel software for real-time analysis and visualization of genetic variants.
  • To enable the identification of genomic regions under balancing selection.
  • To provide a tool for differentiating user-defined groups, such as populations, using genetic markers.

Main Methods:

  • Development of VarB software using C++.
  • Real-time visualization of variant call format (VCF) files.
  • Application of VarB to sequence data from 50 Plasmodium falciparum isolates.

Main Results:

  • VarB successfully visualizes genetic variants in real-time.
  • The software identified regions under balancing selection.
  • Known signals in antigenic and drug-resistance genes were confirmed using P. falciparum data.
  • VarB differentiated between Plasmodium falciparum isolates from different continents.

Conclusions:

  • VarB is an essential tool for real-time analysis and visualization of genetic variants from diverse sequence data.
  • The software aids in understanding population structure and identifying genes under selection.
  • VarB's utility is demonstrated in a biologically relevant context, such as malaria research.