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Ensembl is a bioinformatics research project aiming to "develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes". It is run in a collaboration between the Wellcome Trust Sanger Institute and the European Bioinformatics Institute, an outstation of the European Molecular Biology Laboratory.

Contents 1 Software and data 2 Current species 3 Usage 4 See Also 5 External links

The project is open source - all data and all software that is produced in the project can be freely accessed and used.

Most of the software produced and used is written in the language Perl and is based on the BioPerl infrastructure. The Perl API can be easily employed in other genomic projects e.g. for the annotation of gene or clone lists.

The website code uses an extensible plugins system which allows groups to modify the website for their own data sets, e.g. Vega which stores and displays manual annotation and Gramene which stores plant genomes.

The annotated genomes include most finished vertebrates and selected model organisms. Currently this includes:

• Chordates
  • Mammals: Human, Mouse, Rat, Chimp, Macaque, Dog, Cow, Elephant, Opossum, Rabbit, Armadillo, Tenrec, Guinea pig, Hedgehog, Cat, Tree shrew, Platypus, Micro bat (pre), shrew (pre), horse (pre), bush baby (pre), squirrel (pre), pig (pre)
  • Birds: Chicken
  • Fish: Takifugu rubripes (Fugu), Tetradodon nigroviridis, Danio rerio (Zebrafish), Oryzias latipes (Medaka), Gasterosteus aculeatus (Stickleback)
  • Frog: Xenopus tropicalis
  • Ancient relatives: Ciona intestinalis, Ciona savignyi
• Invertebrates
  • Insects: Anopheles gambiae (Mosquito), Drosophila melanogaster (Fruitfly), Aedes aegypti (Mosquito)
  • Worm: Caenorhabditis elegans
• Yeast: Saccharomyces cerevisiae (Baker's yeast)

The service is used by molecular biologists and bioinformaticians around the world working with genome data of the above organisms. The predictions of coding, controlling and other elements in the genomes can be compared with primary research data and with common repositories of current genomic knowledge (Biological Databases).

The comparison of organisms (comparative genomics or also intergenomics) with respect to their gene structures and the coded proteins is of special interest. The synteny view can be useful educational material for school classes.

• Sequence analysis
• Sequence profiling tool
• Sequence motif

• Ensembl
• Vega
• Pre-Ensembl

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