DoGSD: the dog and wolf genome SNP database - PubMed (original) (raw)

. 2015 Jan;43(Database issue):D777-83.

doi: 10.1093/nar/gku1174. Epub 2014 Nov 17.

Wen-Ming Zhao 2, Bi-Xia Tang 3, Yan-Qing Wang 2, Lu Wang 4, Zhang Zhang 5, He-Chuan Yang 6, Yan-Hu Liu 4, Jun-Wei Zhu 2, David M Irwin 7, Guo-Dong Wang 8, Ya-Ping Zhang 9

Affiliations

DoGSD: the dog and wolf genome SNP database

Bing Bai et al. Nucleic Acids Res. 2015 Jan.

Abstract

The rapid advancement of next-generation sequencing technology has generated a deluge of genomic data from domesticated dogs and their wild ancestor, grey wolves, which have simultaneously broadened our understanding of domestication and diseases that are shared by humans and dogs. To address the scarcity of single nucleotide polymorphism (SNP) data provided by authorized databases and to make SNP data more easily/friendly usable and available, we propose DoGSD (http://dogsd.big.ac.cn), the first canidae-specific database which focuses on whole genome SNP data from domesticated dogs and grey wolves. The DoGSD is a web-based, open-access resource comprising ∼ 19 million high-quality whole-genome SNPs. In addition to the dbSNP data set (build 139), DoGSD incorporates a comprehensive collection of SNPs from two newly sequenced samples (1 wolf and 1 dog) and collected SNPs from three latest dog/wolf genetic studies (7 wolves and 68 dogs), which were taken together for analysis with the population genetic statistics, Fst. In addition, DoGSD integrates some closely related information including SNP annotation, summary lists of SNPs located in genes, synonymous and non-synonymous SNPs, sampling location and breed information. All these features make DoGSD a useful resource for in-depth analysis in dog-/wolf-related studies.

© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Figures

Figure 1.

Figure 1.

The data sources and pipeline to construct DoGSD.

Figure 2.

Figure 2.

The screen dumps of the SNP lists of DoGSD and typical browse results. The curly arrow indicates two steps are not directly linked and the straight arrow means two steps are directly linked. (A) The non-redundant and individual sample SNP lists. (B) The text format browse result of an SNP. (C) GBrowse visualization of a SNP.

Figure 3.

Figure 3.

Example of a comparative search. (A) An example of search entry. (B) The comparative search result.

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