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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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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Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
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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%...
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Genome-wide Association Studies-GWAS01:11

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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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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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...
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Related Experiment Video

Updated: Aug 23, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Animal-SNPAtlas: a comprehensive SNP database for multiple animals.

Yingjie Gao1, Guanghui Jiang1, Wenqian Yang1

  • 1Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China.

Nucleic Acids Research
|October 27, 2022
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Summary

This study identifies 499 million high-quality single-nucleotide polymorphisms (SNPs) across 20 animal species. The Animal-SNPAtlas database provides valuable genetic resources and tools for animal genomics and breeding research.

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Area of Science:

  • Animal Genomics
  • Population Genetics
  • Bioinformatics

Background:

  • Single-nucleotide polymorphisms (SNPs) are crucial for understanding population characteristics and animal genetics.
  • Existing genetic variation databases are more developed for humans than animals, hindering animal genetic research.
  • A comprehensive resource for animal genetic variation is needed.

Purpose of the Study:

  • To systematically identify and characterize millions of high-quality SNPs from diverse animal species.
  • To develop a user-friendly database, Animal-SNPAtlas, integrating SNP data and analytical tools.
  • To support advancements in animal genomics, genetics, and breeding.

Main Methods:

  • Identification of approximately 499 million high-quality SNPs from 4784 samples across 20 animal species.
  • Functional annotation of identified SNPs and construction of high-density reference panels.
  • Calculation of genome-wide linkage disequilibrium (LD) matrixes.

Main Results:

  • The development of Animal-SNPAtlas, a centralized database featuring extensive SNP datasets and analytical tools.
  • The database enables users to search SNP functional annotations, perform genotype imputation, and visualize LD information.
  • Users can browse variant information via a genome browser and download species-specific SNP datasets.

Conclusions:

  • Animal-SNPAtlas provides a massive, high-quality SNP resource and integrated tools for the animal genomics community.
  • This database will significantly facilitate research in animal genetics and breeding.
  • It serves as a fundamental resource for exploring and utilizing animal genetic variation.