Title

Documentation

General

The Ruminant Genome Database (RGD) is a comprehensive repository of integrated genomics, transcriptomics, and epigenetics data of Ruminantia, a suborder which includes economically important livestock: cattle, yak, sheep, and goats. The RGD builds a feature-rich UCSC Genome Browser to the local server, and implements open-source software and MySQL databases providing access to all the data contributed by our Ruminant Genome Project (RGP) and other public database. The current version of the RGD contains data of 54 ruminant genomes, whole genome alignments of 54 ruminants and 12 mammals, five scales of conservative evaluation, 1151 samples of RNA-seq data, as well as regulatory regions predicted by utilizing 32 ruminant epigenomic and 726 human epigenomic datasets. The gene ontology (GO) terms, KEGG pathway, and gene expression heatmap can be queried with gene symbols. RGD also provides online alignment tools such as webBlat and NCBI’s wwwBLAST server against the goat ARS1 assembly. All the data were integrated into UCSC Genome Browser to facilitate global presentation. Collectively, all these features make the RGD a useful archive for in-depth analysis in biology and evolution of ruminants.