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DoGSD: the dog and wolf genome SNP database.

Bai B, Zhao WM, Tang BX, Wang YQ, Wang L, Zhang Z, Yang HC, Liu YH, Zhu JW, Irwin DM, Wang GD, Zhang YP - Nucleic Acids Res. (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Conservation and Utilization of Bioresource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China Kunming College of Life Science, University of Chinese Academy of Sciences,Kunming 650204, China.

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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.
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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.

Mentions: The DoGSD database can be accessed through a simple user interface. Online documentation is provided to help users to access the database. DoGSD has been designed with two main functionalities for data retrieval, Browse and Search. Users may browse the no-redundant and individual sample SNPs either with text format in tables (Figure 2A), or with a chromosome-based graphical GBrowse (24) interface. In the text format tables, SNP ID, sample and sequencing platform information, chromosome location, reference and derived alleles, three-fifths flank sequences are given for each SNP and annotated gene, transcript and protein, derived residual and counterparts from other samples are given if available (Figure 2B). In GBrowse interface, users can obtain Fst values, a pie chart showing the allele frequency of the dog and wolf populations, SNP density in 300 kb windows size, related gene and transcript information (Figure 2C).


DoGSD: the dog and wolf genome SNP database.

Bai B, Zhao WM, Tang BX, Wang YQ, Wang L, Zhang Z, Yang HC, Liu YH, Zhu JW, Irwin DM, Wang GD, Zhang YP - Nucleic Acids Res. (2014)

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.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383968&req=5

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.
Mentions: The DoGSD database can be accessed through a simple user interface. Online documentation is provided to help users to access the database. DoGSD has been designed with two main functionalities for data retrieval, Browse and Search. Users may browse the no-redundant and individual sample SNPs either with text format in tables (Figure 2A), or with a chromosome-based graphical GBrowse (24) interface. In the text format tables, SNP ID, sample and sequencing platform information, chromosome location, reference and derived alleles, three-fifths flank sequences are given for each SNP and annotated gene, transcript and protein, derived residual and counterparts from other samples are given if available (Figure 2B). In GBrowse interface, users can obtain Fst values, a pie chart showing the allele frequency of the dog and wolf populations, SNP density in 300 kb windows size, related gene and transcript information (Figure 2C).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Conservation and Utilization of Bioresource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China Kunming College of Life Science, University of Chinese Academy of Sciences,Kunming 650204, China.

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