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

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

14.6K
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,...
14.6K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

12.6K
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...
12.6K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

11.6K
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%...
11.6K

You might also read

Related Articles

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

Sort by
Same author

Feature representation for explainable CRISPR off-target prediction and base editing efficiency.

Frontiers in bioinformatics·2026
Same author

Uncovering miRNA-Disease Associations Through Graph Based Neural Network Representations.

Biomedicines·2026
Same author

Superficial vs. Deep Venous System in DIEP Flaps: Lessons from 25 Years of CTA-Guided Planning.

Journal of clinical medicine·2025
Same author

Implementation of a Digital Maturity Framework for Biobanking.

Journal of biomedical informatics·2025
Same author

Deciphering the landscape of allosteric glutaminase 1 inhibitors as anticancer agents.

Bioorganic chemistry·2025
Same author

Beyond the Surface: Nutritional Interventions Integrated with Diagnostic Imaging Tools to Target and Preserve Cartilage Integrity: A Narrative Review.

Biomedicines·2025
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026
Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026
Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026
See all related articles

Related Experiment Video

Updated: May 2, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

41.3K

A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units.

Andrea Manconi, Alessandro Orro, Emanuele Manca

    BMC Bioinformatics
    |February 26, 2014
    PubMed
    Summary
    This summary is machine-generated.

    G-SNPM is a GPU-accelerated tool that accurately remaps Single Nucleotide Polymorphisms (SNPs) to their genomic positions. This GPU-based approach enhances SNP mapping for Genome Wide Association Studies (GWAS) and annotation tasks.

    More Related Videos

    A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
    09:10

    A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

    Published on: May 22, 2018

    10.6K
    Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
    09:30

    Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

    Published on: August 17, 2022

    2.1K

    Related Experiment Videos

    Last Updated: May 2, 2026

    Infinium Assay for Large-scale SNP Genotyping Applications
    13:33

    Infinium Assay for Large-scale SNP Genotyping Applications

    Published on: November 19, 2013

    41.3K
    A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
    09:10

    A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

    Published on: May 22, 2018

    10.6K
    Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
    09:30

    Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

    Published on: August 17, 2022

    2.1K

    Area of Science:

    • Genomics
    • Bioinformatics
    • Computational Biology

    Background:

    • Single Nucleotide Polymorphism (SNP) genotyping is prone to chromosomal position errors.
    • Existing SNP mapping data lack accuracy assessment and require updates with new genome builds.
    • Remapping SNPs is crucial for obtaining accurate and up-to-date chromosomal positions.

    Purpose of the Study:

    • To introduce G-SNPM, a novel Graphics Processing Unit (GPU)-based tool for efficient SNP mapping.
    • To address the limitations of current SNP mapping accuracy and data relevance.
    • To provide researchers with an updated and reliable method for SNP localization.

    Main Methods:

    • G-SNPM employs a three-stage pipeline for mapping SNPs to reference DNA sequences.
    • Utilizes GPU-accelerated SOAP3-dp for initial parallel alignment of SNP sequences.
    • Incorporates SHRiMP2 for remapping unaligned or ambiguous sequences, leveraging specialized hardware for speed.
    • Final stage analyzes alignments to determine the absolute physical position of each SNP.

    Main Results:

    • G-SNPM successfully remapped nearly all SNPs from commercial chips without ambiguity.
    • The tool demonstrates fast mapping speeds owing to modern GPU utilization.
    • Accuracy of SNP mapping is maintained or improved by the G-SNPM tool.

    Conclusions:

    • G-SNPM provides an accurate and efficient solution for SNP remapping.
    • The tool is suitable for specialized Genome Wide Association Studies (GWAS).
    • G-SNPM aids in annotation tasks requiring updated SNP mapping probes.