What is Ensembl Genomes?

Ensembl Bacteria, Protists, Fungi, Plants and Metazoa (collectively, ‘Ensembl Genomes’) are five portals for genome-scale data, developed in close collaboration with scientific communities expert in the biology of individual species. Implemented using the Ensembl software suite for genome analysis and browsing, which was developed for the study of vertebrate genomes (described by Flicek et al. 2012, Ensembl 2012, Nucleic Acids Res. 40 D84-90), Ensembl Genomes provides a powerful and consistent set of interactive and programmatic interfaces for non-vertebrate genomes, providing access to data including gene predictions, comparative analysis, variant annotation, and transcriptomic alignments. Since its establishment in 2009, the resource has grown rapidly and now contains 70 eukaryotic and 249 bacterial species. Moreover, recent improvements to the site make it easier than ever to upload your own data and to visualise and analyse it in the context of reference annotations (Figure 1).

The Ensembl Genomes homepage

Figure 1 Ensembl Genomes entry page showing the five portals on the right-hand side.

Data sources

Ensembl Genomes provides access to genome-scale data through a number of interfaces, including a web browser, a search-optimised data warehouse, bulk download and various programmatic interfaces. The data come from a variety of sources, including collaborators in the scientific community, publicly available data archives, and computational analysis pipelines run at the EBI and elsewhere. As the scientific scope of the project is exceptionally broad, our goal is to provide an up-to-date view of core annotation as recognised by the relevent scientific communities, integrated with data from other species through the use of shared interfaces and comparative analysis.

Wherever possible, we actively collaborate with community groups in the management of data and the development of services, including:

We also show cannonical annotations from leading model organism databases such as:

  • DictyBase (for Dictyostelium discoideum)
  • FlyBase (for Drosophila)
  • SGD (for Saccharomyces cerevisiae).