identifiers which are tracked between Ensembl releases.–It provides relationships between genes and genomes in a comparative genomics framework in the form of sequence alignments, ortholog and paralog assignments and genetrees, again generated from an automatic pipeline where no manually curated relationships exist.It is a completely open project, not only through providing downloads of all data and software source code, but through multiple levels of programmatic access: – It allows its database system to be programmed against using the Ensembl API, a powerful object oriented representation of biological entities (e.g. genes) implemented in the Perl programming language.– It allows its genome annotations, alignments, variation and functional genomics data to be dynamically federated with external data sources via the DAS protocol (3,4) and visualized through many of its website interfaces (http://www.ensembl.org/).– It allows its datasets to be dynamically federated with external datasets for data mining using the BioMart system (5). The Ensembl project is now being joined by the Ensembl Genomes project (http://www.ensemblgenomes.org/), which will use Ensembl technology to ultimately provide a common interface to genomes across biology.
