Event: Plant and Animal Genomes Conference
Speaker: Bert Overduin
The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. As of Ensembl release 65 (December 2011), 56 species are fully supported. Ensembl data are accessible through an interactive web site, flat files, the data mining tool BioMart, direct database querying and a set of Perl APIs. Moreover, Ensembl is not just a data visualisation tool, but a suite of programs for data production (e.g. gene calling and comparative genomics) that can be deployed individually according to the needs of an individual community. Ensembl Genomes (http://www.ensemblgenomes.org) consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the genomes available in Ensembl. It currently contains data for over 300 species. Many of the databases that support Ensembl Genomes have been built by, or in close collaboration with, groups that maintain specialist data resources for individual species, and we are actively seeking to extend the range of these collaborations. Together Ensembl and Ensembl Genomes offer a single unified interface across the taxonomic space. This presentation will consist of a short introduction to Ensembl and Ensembl Genomes followed by a demonstration of the respective websites and the BioMart data retrieval tool. Special attention will be given to recently developed functionality like the Variant Effect Predictor, which predicts the consequences of substitutions, insertions and deletions on transcripts and protein sequences, and the possibility to visualize your own data by attaching BAM and VCF files (for example).