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

Single Nucleotide Polymorphisms-SNPs

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,...

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%...

Statistical Package for the Social Sciences (SPSS)

Statistical Package for the Social Sciences (SPSS)

The Statistical Package for the Social Sciences, or SPSS, is a data management and analysis software suite. Developed by SPSS Inc. in 1968 and acquired by IBM in 2009, this tool was initially designed for social science data analysis, evolving to serve a wider range of disciplines. It was later renamed to Statistical Product and Service Solutions.
SPSS streamlines the process from data preparation to analysis and reporting. It is characterized by its user-friendly interface, which conceals...

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...

Punnett Squares

Punnett Squares

Punnett Squares

Punnett Squares

You might also read

Related Articles

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

Sort by

Same author

<i>Pfcrt</i> copy number amplification detected in a <i>Plasmodium falciparum</i> outbreak.

bioRxiv : the preprint server for biology·2026

Same author

Associations between the Plasmodium falciparum genome and sickle haemoglobin identified in mild malaria cases from Ghana.

Malaria journal·2026

Same author

Major features of parasite adaptation revealed by genomes of Plasmodium falciparum population samples archived for over 50 years.

Communications biology·2026

Same author

Pf8: an open dataset of <i>Plasmodium falciparum </i>genome variation in 33,325 worldwide samples.

Wellcome open research·2025

Same author

Microhaplotype deep sequencing assays to capture Plasmodium vivax infection lineages.

Nature communications·2025

Same author

Identification of complex Plasmodium falciparum genetic backgrounds circulating in Africa: a multicountry genomic epidemiology analysis.

The Lancet. Microbe·2024

Search research articles

Related Experiment Video

Updated: Jun 21, 2026

The Visual Colorimetric Detection of Multi-nucleotide Polymorphisms on a Pneumatic Droplet Manipulation Platform

The Visual Colorimetric Detection of Multi-nucleotide Polymorphisms on a Pneumatic Droplet Manipulation Platform

Published on: September 27, 2016

SNP-o-matic.

Heinrich Magnus Manske¹, Dominic P Kwiatkowski

¹Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK. mm6@sanger.ac.uk

Bioinformatics (Oxford, England)

|July 4, 2009

Summary

This summary is machine-generated.

SNP-o-matic is a fast and memory-efficient tool for mapping short DNA reads. It minimizes errors in alignments, improving genotyping accuracy for high-throughput sequencing data.

More Related Videos

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Multi-Gene Single Nucleotide Polymorphism Detection in Gastric Cancer Based on Ion Semiconductor Sequencing Platform

Multi-Gene Single Nucleotide Polymorphism Detection in Gastric Cancer Based on Ion Semiconductor Sequencing Platform

Published on: May 10, 2024

Related Experiment Videos

Last Updated: Jun 21, 2026

The Visual Colorimetric Detection of Multi-nucleotide Polymorphisms on a Pneumatic Droplet Manipulation Platform

The Visual Colorimetric Detection of Multi-nucleotide Polymorphisms on a Pneumatic Droplet Manipulation Platform

Published on: September 27, 2016

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Multi-Gene Single Nucleotide Polymorphism Detection in Gastric Cancer Based on Ion Semiconductor Sequencing Platform

Multi-Gene Single Nucleotide Polymorphism Detection in Gastric Cancer Based on Ion Semiconductor Sequencing Platform

Published on: May 10, 2024

Area of Science:

Genomics
Bioinformatics

Background:

High-throughput sequencing generates vast amounts of short DNA reads.
Read mapping to reference sequences is computationally intensive and prone to errors.
Existing tools can be slow, memory-hungry, and produce inaccurate alignments.

Purpose of the Study:

Introduce SNP-o-matic, a novel read mapping tool.
Address the computational challenges of short read mapping.
Enhance the accuracy and efficiency of genotyping.

Main Methods:

Developed SNP-o-matic as a fast and memory-efficient read mapper.
Implemented stringent mapping criteria to reduce errors.
Integrated diverse analytical output functions, focusing on genotyping.

Main Results:

SNP-o-matic demonstrates superior speed and memory efficiency compared to existing tools.
The tool achieves high accuracy in read mapping and alignment.
Effective in producing reliable genotyping data from sequencing reads.

Conclusions:

SNP-o-matic offers a robust solution for processing large-scale sequencing data.
The tool significantly improves the efficiency and accuracy of bioinformatics pipelines.
Recommended for genotyping applications requiring precise and fast read mapping.