Bovine Genome Database: new annotation tools for a new reference genome.
Md Shamimuzzaman1, Justin J Le Tourneau1, Deepak R Unni2
1Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
Nucleic Acids Research
|October 25, 2019
Summary
The Bovine Genome Database (BGD) now offers enhanced tools and datasets for bovine genomics research. Updates include improved genome assembly error detection and expanded data for related ruminant species.
Area of Science:
- Genomics
- Bioinformatics
- Comparative Genomics
Background:
- The Bovine Genome Database (BGD) has served as a central resource for bovine genomics for over ten years.
- Increasing data volume and complexity necessitate continuous improvements in data management and accessibility.
Purpose of the Study:
- To enhance the Bovine Genome Database (BGD) with advanced tools and expanded datasets for the research community.
- To improve data acquisition, curation, integration, and retrieval processes.
Main Methods:
- Developed a new Apollo plug-in, the Locus-Specific Alternate Assembly (LSAA) tool, for identifying genome assembly errors and structural variants.
- Integrated the newest bovine reference genome assembly (ARS-UCD1.2) alongside the previous version (UMD3.1.1).
- Expanded BovineMine with genomes and gene annotations for goat and sheep, and enhanced search functionalities.
Main Results:
- BGD now supports cross-genome navigation between ARS-UCD1.2 and UMD3.1.1 assemblies.
- The LSAA tool enables users to report potential genome assembly errors and structural variants.
- BovineMine now includes data for non-bovine ruminants and supports multiple assemblies per organism.
Conclusions:
- BGD continues to evolve, offering improved tools and comprehensive datasets for bovine and ruminant genomics.
- Ongoing development focuses on enhancing existing resources and introducing new functionalities to support scientific discovery.
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