Database Commons
Database Commons

a catalog of worldwide biological databases

Database Profile

General information

URL: http://animal.nwsuaf.edu.cn/BosVar
Full name: Bovine Genome Variation Database
Description: BGVD provides six main functionalities: gene search, variation search, genomic signature search, Genome Browser, alignment search tools, and the genome coordinate conversion tool. BGVD contains information on genomic variations comprising ~60.44 M SNPs, ~6.86 M indels, 76,634 CNV regions, and signatures of selective sweeps in 432 samples from modern cattle worldwide.
Year founded: 2020
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Country/Region: China

Classification and Labelling

Data type:
DNA
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Contact information

University/Institution: Northwest A&F University
Address:
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Country/Region: China
Contact name (PI/Team): Yu Jiang
Contact email (PI/Helpdesk): yu.jiang@nwafu.edu.cn

Publications

32540200
BGVD: An Integrated Database for Bovine Sequencing Variations and Selective Signatures. [PMID: 32540200]
Ningbo Chen, Weiwei Fu, Jianbang Zhao, Jiafei Shen, Qiuming Chen, Zhuqing Zheng, Hong Chen, Tad S Sonstegard, Chuzhao Lei, Yu Jiang

Next-generation sequencing has yielded a vast amount of cattle genomic data for global characterization of population genetic diversity and identification of genomic regions under natural and artificial selection. However, efficient storage, querying, and visualization of such large datasets remain challenging. Here, we developed a comprehensive database, the Bovine Genome Variation Database (BGVD). It provides six main functionalities: gene search, variation search, genomic signature search, Genome Browser, alignment search tools, and the genome coordinate conversion tool. BGVD contains information on genomic variations comprising ~60.44 M SNPs, ~6.86 M indels, 76,634 CNV regions, and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map, using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection sweep are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data, and resources, from NCBI, the UCSC Genome Browser, and Animal QTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale. BGVD is publicly available at http://animal.nwsuaf.edu.cn/BosVar.

Genomics Proteomics Bioinformatics. 2020:() | 5 Citations (from Europe PMC, 2022-08-13)

Ranking

All databases:
2565/5379 (52.333%)
Gene genome and annotation:
747/1429 (47.796%)
2565
Total Rank
5
Citations
2.5
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Record metadata

Created on: 2022-07-30
Curated by:
Zhang Zhang [2022-07-30]