The Ensembl Farm: All You Need Is Livestock

Ensembl enables genomic science by providing high-quality, integrated annotation on livestock and other vertebrate genomes within a consistent and accessible infrastructure.

With the recent addition of sheep, we provide genomic and functional annotation for a wide range of livestock, which also includes cattle, pig and chicken. For each of these species, the Ensembl pipelines generated protein coding and non-coding RNA models using publicly available protein and nucleic acid sequence data from resources such as UniProt and ENA.

Transcriptome data are available for some species. Our most comprehensive transcriptome data set is for sheep, where we have data for over 90 tissue samples from a trio (ram, ewe and lamb). These data sets give insight into expression levels and alternative isoforms as we provide tissue-specific gene models, raw RNASeq read alignments and splice site read coverage.

In addition to gene annotation, we produce orthologues and we include variation and gene regulation data where available. Embedded comparative and variation tools allow inter- and intra-species analyses giving the best information available to our users.

Genome annotation for livestock species is available at www.ensembl.org and can be queried using BLAST, BioMart, VEP, WiggleTools and our new REST API. Users can compare and analyse their own data by uploading files such as BAM files or using TrackHubs.

All of our data and software are open source. Data files can be downloaded from ftp.ensembl.org and our Perl API code can be downloaded from https://github.com/Ensembl