The Bovine Genome Database supports the efforts of bovine genomics researchers by providing data mining, genome navigation and annotation tools for the bovine reference genome based on the hereford cow, L1 Dominette 01449.
BGD provides tools for data mining (BovineMine), sequence database searching (BLAST), genome browsing (JBrowse) and annotation (Apollo). The bovine reference genome assembly has been revised several times. The newest release of BovineMine (BovineMine v1.6) includes both the ARS-UCD1.2 and UMD3.1 genome assemblies, and the last release with only UMD3.1.1 (BovineMine v1.4) is still available. JBrowse is also available for both ARS-UCD1.2 and UMD3.1.
BovineMine integrates the genome assemblies with a variety of data sources, including genes, proteins, orthologs, pathways, gene ontology, gene expression, interactions, variants, QTL and publications. The goal of BovineMine is to accelerate genomics analysis by enabling researchers without scripting skills to create and export customized annotation datasets merged with their own research data for use in downstream analyses. BovineMine allows researchers to leverage the curated gene pathways of model organisms (e.g. human, mouse and rat) based on orthology, and is especially useful for GO and pathway analyses in conjunction with GWAS and QTL studies. BovineMine also includes reference genomes of sheep and goat so researchers can leverage information across ruminants.
A chapter on Bovine Genome Database in the Methods in Molecular Biology volume "Eukaryotic Genomic Databases" focuses on BovineMine:
Hagen D.E., Unni D.R., Tayal A., Burns G.W., Elsik C.G. (2018) Bovine Genome Database: Tools for Mining the Bos taurus Genome. In: Kollmar M. (eds) Eukaryotic Genomic Databases. Methods in Molecular Biology, vol 1757. Humana Press, New York, NY. doi: 10.1007/978-1-4939-7737-6_9
Please cite the use of BGD, including BovineMine, JBrowse, Apollo, BLAST and other BGD tools:
Elsik CG, Unni DR, Diesh CM, Tayal A, Emery ML, Nguyen HN, Hagen DE. Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. Nucleic Acids Res. 2016 Jan 4;44(D1):D834-9. doi: 10.1093/nar/gkv1077. Epub 2015 Oct 19. PubMed PMID: 26481361.