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Animal-SNPAtlas: a comprehensive SNP database for multiple animals
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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825464/ https://www.ncbi.nlm.nih.gov/pubmed/36300636 http://dx.doi.org/10.1093/nar/gkac954 |
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author | Gao, Yingjie Jiang, Guanghui Yang, Wenqian Jin, Weiwei Gong, Jing Xu, Xuewen Niu, Xiaohui |
author_facet | Gao, Yingjie Jiang, Guanghui Yang, Wenqian Jin, Weiwei Gong, Jing Xu, Xuewen Niu, Xiaohui |
author_sort | Gao, Yingjie |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9825464 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-98254642023-01-10 Animal-SNPAtlas: a comprehensive SNP database for multiple animals Gao, Yingjie Jiang, Guanghui Yang, Wenqian Jin, Weiwei Gong, Jing Xu, Xuewen Niu, Xiaohui Nucleic Acids Res Database Issue 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. Oxford University Press 2022-10-27 /pmc/articles/PMC9825464/ /pubmed/36300636 http://dx.doi.org/10.1093/nar/gkac954 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Gao, Yingjie Jiang, Guanghui Yang, Wenqian Jin, Weiwei Gong, Jing Xu, Xuewen Niu, Xiaohui Animal-SNPAtlas: a comprehensive SNP database for multiple animals |
title | Animal-SNPAtlas: a comprehensive SNP database for multiple animals |
title_full | Animal-SNPAtlas: a comprehensive SNP database for multiple animals |
title_fullStr | Animal-SNPAtlas: a comprehensive SNP database for multiple animals |
title_full_unstemmed | Animal-SNPAtlas: a comprehensive SNP database for multiple animals |
title_short | Animal-SNPAtlas: a comprehensive SNP database for multiple animals |
title_sort | animal-snpatlas: a comprehensive snp database for multiple animals |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825464/ https://www.ncbi.nlm.nih.gov/pubmed/36300636 http://dx.doi.org/10.1093/nar/gkac954 |
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