For each organism supported by Ensembl, a species-specific Ensembl Core database stores the bulk of annotation information. Some of the key features are:
Human and Mouse have a separate cDNA database, containing alignments of all species-specific cDNAs to the genome sequence, which serve as source of biological evidence in the Ensembl annotation strategy. The alignments are updated every release and should therefore include even the most recently submitted cDNA sequences.
For human and mouse, the otherfeatures database contains the full set of species-specific EST alignments to the genome. For all other species with enough species-specific data, the otherfeatures database contains the full set of species-specific cDNA and EST alignments to the genome.
For well-characterised species with a reasonable amount of biological sequence records as supporting evidence Ensembl provides an independent EST gene set, which is solely based on EST information.
Please note that Ensembl OtherFeatures databases do not contain genome sequences. This saves disk space and by connecting to Core and the OtherFeatures databases simultaneously, it is still possible to retrieve sequence information.
The layout of Ensembl Core and OtherFeature databases is identical so that schema descriptions and API access apply similarly. The database table layout is explained in the following document:
A comprehensive Perl Application Programme Interface (API) provides efficient access to tables within the Ensembl Core and EST databases.
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