Bovine Genome Database: 2012 Update

The bovine genome sequence provides tremendous potential to discover genetic mechanisms underlying important livestock traits. However, to realize this potential, the genome information must be made accessible to livestock researchers. The Bovine Genome Database (BGD, http://bovinegenome.org) facilitates access to Bos taurus genome assemblies and annotation. Users may access data through genome browsers (Gbrowse), the Apollo Annotation Editor, BLAST searching, and gene query interfaces. Genome browsers, provided on both scaffold and chromosome coordinate systems, display gene predictions, non-coding RNA, repeats, pseudogenes, SNPs, markers, QTL and alignments to cDNAs, ESTs, and protein homologs. Gene pages display information for individual OGS gene models, including gene structure, transcript variants, functional descriptions, gene symbols, gene ontology, annotator comments and references to external databases. Users may search by gene symbol, annotator, GO term or BGD identifier. Each gene page is linked to a wiki page to allow input from the research community. Recent additions to BGD include genome browsers for alternate Bos taurus assemblies, and a system to navigate across alternate assemblies. In addition to new assembly data, we have enhanced the BGD Chado database schema and supporting infrastructure to generate audit reports to track revisions, and we have further developed the Bovine QTL database by extending our previous JAVA based object oriented framework that allows mapping of complex queries to the BGD Chado schema.