Ensembl
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Ensembl is a bioinformatics research project precisely a Genome Browser 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.
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. But users always find this a pain to deploy and use as it has so many conf files and so many versions that gets released more often than one can keep up with updating.
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.
Current species
The annotated genomes include most finished vertebrates and selected model organisms. Currently this includes:
- Chordates
- Mammals: Armadillo, Bush baby, Cat, Chimp, Cow, Dog, Elephant, Guinea pig, Hedgehog, Human, Macaque, Micro bat, Mouse, Opossum, Platypus, Rabbit, Rat, shrew, squirrel, Tenrec, Tree shrew, horse (pre), mouse lemur (pre), pig (pre), pika (pre)
- Birds: Chicken
- Fish: Fugu, Tetradodon nigroviridis, Zebrafish, Medaka, Stickleback, Lamprey (pre)
- Lizard: Anole Lizard (pre)
- Frog: Xenopus tropicalis
- Ancient relatives: Ciona intestinalis, Ciona savignyi
- Invertebrates
- Insects: Anopheles gambiae (Mosquito), Fruitfly, Aedes aegypti (Mosquito)
- Worm: Caenorhabditis elegans
- Yeast: Saccharomyces cerevisiae (Baker's yeast)
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.
See Also
External links
de:Ensemblfr:Ensembl it:Ensembl nl:Ensembl
Acknowledgement and Attribution Regarding Sources of Content
Some of the initial content on this page may be incorporated in part from copyleft sources in the public domain including wikis such as Wikipedia and AskDrWiki. Drug information for patients came from the The National Library of Medicine. Infectious disease information may have come from the Centers for Disease Control (CDC). Differential Diagnoses are drawn from clinicians as well as an amalgamation of 3 sources: 1.The Disease Database; 2. Kahan, Scott, Smith, Ellen G. In A Page: Signs and Symptoms. Malden, Massachusetts: Blackwell Publishing, 2004:3; 3. Sailer, Christian, Wasner, Susanne. Differential Diagnosis Pocket. Hermosa Beach, CA: Borm Bruckmeir Publishing LLC, 2002:7 .
