Bovine Genome Database: new annotation tools for a new reference genome.

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Tytuł:: Bovine Genome Database: new annotation tools for a new reference genome.
Autorzy:: Shamimuzzaman M; Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
Le Tourneau JJ; Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
Unni DR; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA.
Diesh CM; Department of Bioengineering, University of California, Berkeley, CA 94720, USA.
Triant DA; Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
Walsh AT; Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
Tayal A; Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.
Conant GC; Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA.; Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA.; Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA.
Hagen DE; Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
Elsik CG; Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.; Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA.; MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA.
Źródło:: Nucleic acids research [Nucleic Acids Res] 2020 Jan 08; Vol. 48 (D1), pp. D676-D681.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
Język:: English
Imprint Name(s):: Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
MeSH Terms:: Databases, Factual*
Genome*
Cattle/*genetics
Computational Biology/*methods
Algorithms ; Animals ; Computer Graphics ; Data Mining ; Databases, Genetic ; Gene Expression Profiling ; Genomics ; Internet ; Molecular Sequence Annotation ; RNA-Seq ; Reference Values ; Ruminants/genetics ; Sequence Alignment ; Software ; User-Computer Interface
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Entry Date(s):: Date Created: 20191025 Date Completed: 20200527 Latest Revision: 20200527
Update Code:: 20240104
PubMed Central ID:: PMC7145693
DOI:: 10.1093/nar/gkz944
PMID:: 31647100
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The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval. BGD provides tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and sequence database searching (BLAST). To augment the BGD genome annotation capabilities, we have developed a new Apollo plug-in, called the Locus-Specific Alternate Assembly (LSAA) tool, which enables users to identify and report potential genome assembly errors and structural variants. BGD now hosts both the newest bovine reference genome assembly, ARS-UCD1.2, as well as the previous reference genome, UMD3.1.1, with cross-genome navigation and queries supported in JBrowse and BovineMine, respectively. Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism in the Regions Search tool, integration of additional ontologies and development of many new template queries. To better serve the research community, we continue to focus on improving existing tools, developing new tools, adding new datasets and encouraging researchers to use these resources.
(© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)

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