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BGVD: An Integrated Database for Bovine Sequencing Variations and Selective Signatures

Ningbo Chen, Weiwei Fu, Jianbang Zhao, Jiafei Shen, Qiuming Chen, Zhuqing Zheng, Hong Chen, Tad S. Sonstegard, Chuzhao Lei, Yu Jiang
2020 Genomics, Proteomics & Bioinformatics  
However, efficient storage, querying, and visualization of such large datasets remain challenging. Here, we developed a comprehensive database, the Bovine Genome Variation Database (BGVD).  ...  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  ...  Acknowledgments The project was supported by the National Natural Science Foundation of China (Grant No. 31822052), and the National Thousand Youth Talents Plan, China (Grant No.  ... 
doi:10.1016/j.gpb.2019.03.007 pmid:32540200 pmcid:PMC7646086 fatcat:hway2mwgh5cobnyn6yjsrsdt3u

The Bovine Genome Variation Database (BGVD): Integrated Web-database for Bovine Sequencing Variations and Selective Signatures [article]

Ningbo Chen, Weiwei Fu, Jianbang Zhao, Jiafei Shen, Qiuming Chen, Zhuqing Zheng, Hong Chen, Tad S. Sonstegard, Chuzhao Lei, Yu Jiang
2019 bioRxiv   pre-print
Here, we developed a comprehensive Bovine Genome Variation Database (BGVD, http://animal.nwsuaf.edu.cn/BosVar) that provides six main functionalities: Gene Search, Variation Search, Genomic Signature Search  ...  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  ...  Here, we develop the Bovine Genome Variation Database (BGVD), the first web-based 72 public database for accessing dense and broadly representative bovine whole-genome variation 73 data.  ... 
doi:10.1101/802223 fatcat:22bt56qj55acpnf7xgg56l7jnq

A Novel SNP in EIF2AK4 Gene Is Associated with Thermal Tolerance Traits in Chinese Cattle

Kaiyue Wang, Yanhong Cao, Yu Rong, Qingqing Ning, Peng Jia, Yongzhen Huang, Xianyong Lan, Ruihua Dang, Hong Chen, Chuzhao Lei
2019 Animals  
and Selective Signatures (BGVD).  ...  A missense single-nucleotide polymorphism (SNP) (NC_037337.1 g.35615224 T > G) in exon 6 of the EIF2AK4 gene which encodes a p.Ile205Ser substitution was observed in the Bovine Genome Variation Database  ...  In the present work, we screened SNPs in the EIF2AK4 gene in the database of the Bovine Genome Variation Database and Selective Signatures (BGVD) (http://animal.nwsuaf.edu.cn/code/index.php/ BosVar) to  ... 
doi:10.3390/ani9060375 pmid:31248194 pmcid:PMC6617145 fatcat:7rh7vqempzhjjapsgaep3kw7qu

Four Novel SNPs of MYO1A Gene Associated with Heat-Tolerance in Chinese Cattle

Peng Jia, Cuicui Cai, Kaixing Qu, Ningbo Chen, Yutang Jia, Quratulain Hanif, Jianyong Liu, Jicai Zhang, Hong Chen, Bizhi Huang, Chuzhao Lei
2019 Animals  
In our study, four novel candidate SNPs highly conserved in B. indicus breeds but barely existed in B. taurus were identified in MYO1A gene according to Bovine Genome Variation Database and Selective Signatures  ...  These SNPs could be used as candidates for marker-assisted selection (MAS) in cattle breeding.  ...  Furthermore, rs209999142 and Figure 1 . 1 Loci and sequencing maps of the four SNPs in bovine MYO1A gene. Figure 1 .Figure 2 . 12 Loci and sequencing maps of the four SNPs in bovine MYO1A gene.  ... 
doi:10.3390/ani9110964 pmid:31766183 pmcid:PMC6912737 fatcat:23mxndmjnzdinabpmsg7muqqou