Ensembl

From Wikipedia, the free encyclopedia

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.

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

[edit] Software and data

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.

Also available is an API in Java.

[edit] Current species

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

Chordates
- Mammals: Human, Mouse, Rat, Chimp, Macaque, Dog, Cow, Elephant (pre), Opossum, Rabbit (preliminary data), Armadillo (pre), Tenrec (pre)
- Birds: Chicken
- Fish: Takifugu rubripes (Fugu), Tetradodon nigroviridis, Danio rerio (Zebrafish)
- Frog: Xenopus tropicalis
- Ancient relatives: Ciona intestinalis, Ciona savignyi (pre)
Invertebrates
- Insects: Anopheles gambiae (Mosquito), Honeybee, Drosophila melanogaster (Fruitfly), Aedes aegypti (Mosquito)
- Worm: Caenorhabditis elegans
Yeast: Saccharomyces cerevisiae (Baker's yeast)

[edit] Usage

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.