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. 2023 Jan 6;51(D1):D816-D826.
doi: 10.1093/nar/gkac954.

Animal-SNPAtlas: a comprehensive SNP database for multiple animals

Yingjie Gao  1 , Guanghui Jiang  1 , Wenqian Yang  1 , Weiwei Jin  1 , Jing Gong  1   2 , Xuewen Xu  3 , Xiaohui Niu  1
Affiliations

Animal-SNPAtlas: a comprehensive SNP database for multiple animals

Yingjie Gao et al. Nucleic Acids Res. .

Abstract

Single-nucleotide polymorphisms (SNPs) as the most important type of genetic variation are widely used in describing population characteristics and play vital roles in animal genetics and breeding. Large amounts of population genetic variation resources and tools have been developed in human, which provided solid support for human genetic studies. However, compared with human, the development of animal genetic variation databases was relatively slow, which limits the genetic researches in these animals. To fill this gap, we systematically identified ∼ 499 million high-quality SNPs from 4784 samples of 20 types of animals. On that basis, we annotated the functions of SNPs, constructed high-density reference panels and calculated genome-wide linkage disequilibrium (LD) matrixes. We further developed Animal-SNPAtlas, a user-friendly database (http://gong_lab.hzau.edu.cn/Animal_SNPAtlas/) which includes high-quality SNP datasets and several support tools for multiple animals. In Animal-SNPAtlas, users can search the functional annotation of SNPs, perform online genotype imputation, explore and visualize LD information, browse variant information using the genome browser and download SNP datasets for each species. With the massive SNP datasets and useful tools, Animal-SNPAtlas will be an important fundamental resource for the animal genomics, genetics and breeding community.

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Figures

Figure 1.
Figure 1.
Flow chart of the Animal-SNPAtlas database.
Figure 2.
Figure 2.
Overview of the Animal-SNPAtlas database. (A) Main modules in Animal-SNPAtlas, including ‘SNP’, ‘Imputation’, ‘Linkage Disequilibrium’, ‘Visualization’ and ‘Download’ modules. (B) The search results of SNPs based on genomic region. (C) SNP annotation information. (D) Online genotype imputation in the Animal-SNPAtlas database.
Figure 3.
Figure 3.
Visualization of the ‘Linkage Disequilibrium’ module. (A) The search box of Linkage Disequilibrium (LD) based on gene ID and genomic region. (B) The search results of LD based on gene ID. (C) The triangular correlation heatmap of the LD matrix.
Figure 4.
Figure 4.
JBrowse Visualization of SNPs in the Animal-SNPAtlas database. (A) Display the context of JBrowse in specific genomic regions. (B, C) Information of the specific SNV.
See this image and copyright information in PMC

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