bovinegenome.elsiklab.missouri.edu Open in urlscan Pro
128.206.116.6  Public Scan

Form analysis
0 forms found in the DOM

Text Content

Skip to main content
BovineGenome.org
The Bovine Genome Database



MAIN NAVIGATION

 * Home
 * BovineMine
   * BovineMine v1.6 (newest)
 * BLAST
 * JBrowse
   * ARS-UCD1.2 JBrowse
 * Apollo
   * Apollo Registration
   * Bovine Apollo Demo
 * Downloads
   * ARS-UCD1.2 Downloads
 * Reference Genome History
 * Cite BGD
 * BGD Publications
 * Elsik Lab Home


THE BOVINE GENOME DATABASE

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. BovineMine v1.6 includes both
the ARS-UCD1.2 and UMD3.1 genome assemblies. 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

A free preprint is available here.

Please cite the use of BGD, including BovineMine, JBrowse, Apollo, BLAST and
other BGD tools:  
Shamimuzzaman M, Le Tourneau JJ, Unni DR, Diesh CM, Triant DA, Walsh AT, Tayal
A, Conant GC, Hagen DE, Elsik CG, Bovine Genome Database: new annotation tools
for a new reference genome, Nucleic Acids Research, gkz944,
https://doi.org/10.1093/nar/gkz944 [Advanced Access]

 

The Bovine Genome Database is supported by the European Union's Seventh
Framework Programme for research, technological development and demonstration
under grant agreement no. 613689, and has been supported by grants
2007-35616-17882, 2010-65205-20407 and 2013-67015-21202 from the USDA National
Institute of Food and Agriculture. BGD is hosted at the University of Missouri.
If you have comments or if you wish to report a problem, please contact the
Bovine Genome Database Administrator.

Photos courtesy of USDA NRSC and Mike MacNeil, USDA/ARS Fort Keogh LARRL.

Site Administration