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14-September-2008 18:02:42 - Ensembl The tone or style of this article or section may not be appropriate for . Specific concerns may be found on the talk page. See 's guide to writing better articles for suggestions. December 2007 Ensembl is a joint project between European Molecular Biology Laboratory EMBL - European Bioinformatics Institute EBI and the Wellcome Trust Sanger Institute WTSI to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. The project consists of: A database schema and associated API to store genomic information; Extension databases to represent functional, comparative and variational genomics; A genebuild pipeline which takes sequence data and builds gene models; Databases containing information for approximately 40 genomes; A website for which users can browse this information; An FTP site which stores the release data along with dumps of genomic sequence and it's associated annotation; Public MySQL instances containing copies of the databases behind the Ensembl website. The project is based at the Wellcome Trust Genome Campus, Hinxton, United Kingdom. Contents 1 Goals of Ensembl 2 Commitments of Ensembl 3 Software and data 3.1 Ensembl API 3.2 Ensembl website 3.3 Ensembl pipeline 4 Current species 5 Usage 6 See also 7 External links Goals of Ensembl The Ensembl project aims to provide: Accurate, automatic analysis of genome data. Analysis and annotation maintained on the current data. Presentation of the analysis to all via the web. Distribution of the analysis to other bioinformatics laboratories. The initial Ensembl project concentrates on vertebrate genomes. A new project Ensembl Genomes based at the EBI will be extending the project into plants, bacteria, protists and metazoa. Additionally a number of other projects use some or all of the parts of the Ensembl project to represent their data. Commitments of Ensembl The commitments of the Ensembl project are: Release of data and analysis into the public domain immediately. Open, collaborative software development: Ensembl imposes no restrictions on access to, or use of, the data provided and the software used to analyse and present it. For more details see the code licence and disclaimer. Collaboration on agreed standards for distribution. Timely development. 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 and Gramene which stores plant genomes. Ensembl API Ensembl website Currently the Ensembl website is undergoing a significant re-design - with the release of the fifth incarnation of the Ensembl website design. The website is, as most of the Ensembl code, written in the Perl scriting language, and runs using mod_perl under Apache. The main websites all run on Unix Linux architecture. The webcode is extensible - using a plugin based system to allow the code to be easily extended. The code is written around a Factory/Object/Configuration/Component model modified MVC. Ensembl pipeline Current species The annotated genomes include most fully sequenced vertebrates and selected model organisms. All of them are eukaryotes, there are no prokaryotes. Currently this includes: Chordates Mammals Primates: Bush baby, Chimp, Human, Macaque, Mouse Lemur, Orangutan Rodents etc.: Guinea Pig, Mouse, Pika, Rabbit, Rat, Squirrel, Tree shrew Laurasiatheria: Cat, Cow, Dog, Hedgehog, Horse, Microbat, Shrew, Pig pre Afrotheria: Elephant, Lesser hedgehog tenrec Xenarthra: Armadillo Marsupials Monotremes: Opossum, Platypus Birds: Chicken Fish: Takifugu rubripes Fugu, Tetraodon nigroviridis Green spotted pufferfish, Danio rerio Zebrafish, Oryzias latipes Medaka, Gasterosteus aculeatus Stickleback, Petromyzon marinus Sea lamprey pre Reptiles Amphibians: Xenopus tropicalis, Anole Lizard pre 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 Sequence analysis Sequence profiling tool Sequence motif v d e Databases supported by Bioinformatic Harvester NCBI-BLAST · CDD · Ensembl · Entrez · Flybase · Flymine · GFP-cDNA · Genome browser · GeneCard · Google Scholar · GoPubMed · HomoloGene · iHOP · IPI · OMIM · MGI · Mitocheck · PSORT · PolyMeta · RGD · UniProt · SOURCE · SOSUI · RZPD · Sciencenet · STRING · SMART · TAIR · WikiProfessional · ZFIN External links Ensembl Vega Pre-Ensembl Ensembl genomes This bioinformatics-related article is a stub. Retrieved from http://en..org/wiki/Ensembl Categories: Bioinformatics | Bioinformatics databases | Bioinformatics stubsHidden categories: All articles needing style ing | articles needing style ing from December 2007 Views Article Discussion this page History Personal tools Log in / create account Navigation Main page Contents Featured content Current events Random article Search Go Search Interaction Community portal Recent changes Contact Donate to Help Toolbox What links here Related changes Upload file Special pages Printable version Permanent link Cite this page Languages Deutsch Español Français Italiano 中文 This page was last modified on 23 June 2008, at 13:25
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