Bovine Genome Database: integrated tools for genome annotation and discovery

Abstract

The Bovine Genome Database (BGD; http://BovineGenome.org) strives to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome browsers, available for both scaffold and chromosome coordinate systems, display the bovine Official Gene Set (OGS), RefSeq and Ensembl gene models, non-coding RNA, repeats, pseudogenes, single-nucleotide polymorphism, markers, QTL and alignments to complementary DNAs, ESTs and protein homologs. The Bovine QTL viewer is connected to the BGD Chromosome GBrowse, allowing for the identification of candidate genes underlying QTL. The Apollo Annotation Editor connects directly to the BGD Chado database to provide researchers with remote access to gene evidence in a graphical interface that allows editing and creating new gene models. Researchers may upload their annotations to the BGD server for review and integration into the subsequent release of the OGS. Gene pages display information for individual OGS gene models, including gene structure, transcript variants, functional descriptions, gene symbols, Gene Ontology terms, annotator comments and links to National Center for Biotechnology Information and Ensembl. Each gene page is linked to a wiki page to allow input from the research community.

Characterisation and expression profile of the bovine cathelicidin gene repertoire in mammary tissue

“…Genomic DNA corresponding to these putative cathelicidins was used for prediction of intron/exon boundaries with GenScan software (Figure 3 ) before the additional predicted cathelicidin sequences were compared with those proposed by previous authors [ 35 , 36 ] (Figure 2 ). ClustalW, in MEGA 5.2 [ 39 ], was used to align the additional cathelicidin sequences found in our analysis with the CATHL8 , CATHL9 and CATHL10 genes described by Elsik et al [ 35 ], as downloaded from the Bovine Genome Database ( http://www.bovinegenome.org [ 40 ]). CATHL8 corresponds with the partial copy of the single intact gene we found.…”

“…The three predicted putative cathelicidin sequences located bioinformatically were compared with those published in previous bioinformatic analyses of this gene cluster. Predicted genes described by Elsik et al [ 35 ] were downloaded from the Bovine Genome Project database ( http://www.bovinegenome.org ; [ 40 ]). DNA sequences for the putative CATHL2L , CATHL3L1 and CATHL3L2 genes published by Dawson et al [ 36 ] were downloaded from the UCSC genome browser using the co-ordinates for the referenced ENSEMBL sequence tags.…”

Genome-wide association study for female fertility in Nordic Red cattle

“…To date information on genomic structure of organisms which are better annotated like mouse and human are used as an information source. However it has been shown that areas which contain mainly regulatory elements and non-protein coding regions the annotation are more challenging [ 25 , 26 ].…”

Significance, Origin, and Function of Bovine Milk Proteins: The Biological Implications of Manipulation or Modification

“…Using classical genetic and molecular genetic approaches, researchers had mapped over 1000 bovine genes by the mid-1990s. For example, the Bovine Genome Database provides an online resource for the analysis and interpretation of the bovine genome (Childers, 2011). Subsequently, the sequencing strategy employed for the bovine genome sequencing project combined the use of bacterial artificial chromosome sequences with a whole genome shotgun sequencing approach, using an individual Hereford cow as the source of DNA.…”