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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

14.9K
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,...
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Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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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%...
17.7K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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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...
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Related Experiment Video

Updated: Jun 17, 2025

Infinium Assay for Large-scale SNP Genotyping Applications
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Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

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Publication-ready single nucleotide polymorphism visualization with snipit.

Áine O'Toole1, Ammar Aziz2, Daniel Maloney1

  • 1Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, EH93FL, United Kingdom.

Bioinformatics (Oxford, England)
|August 13, 2024
PubMed
Summary

Snipit is a user-friendly tool for analyzing and visualizing single nucleotide polymorphisms (SNPs) in DNA sequences. It helps researchers easily compare sequences and identify genetic variations with customizable, publication-ready figures.

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Last Updated: Jun 17, 2025

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accurate analysis of single nucleotide polymorphisms (SNPs) is crucial for understanding genetic variation.
  • Visualizing sequence differences and recombination patterns can be challenging with existing tools.

Purpose of the Study:

  • To introduce Snipit, an open-source Python-based tool for summarizing and visualizing SNPs.
  • To provide researchers with a user-friendly platform for sequence comparison and analysis.

Main Methods:

  • Snipit catalogues nucleotide and amino acid differences against a reference sequence.
  • The tool offers customizable features including color palettes, record sorting, and multiple output formats.
  • A specialized 'recombi-mode' is included for visualizing recombination patterns.

Main Results:

  • Snipit enables efficient comparison of sequences, highlighting genetic variations.
  • Customizable figures facilitate clear and publication-ready data presentation.
  • The recombi-mode effectively illustrates complex sequence relationships.

Conclusions:

  • Snipit provides a versatile and accessible solution for SNP analysis and visualization.
  • The tool supports researchers across various disciplines by simplifying complex genetic data interpretation.
  • Its open-source nature and comprehensive features enhance its utility in genomic research.