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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". Bioinformatics is the application of information technology to the field of molecular biology 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. The Wellcome Trust Sanger Institute (formerly the Sanger Centre is a Genome research centre in the Wellcome Trust Genome Campus in Cambridgeshire, The European Bioinformatics Institute (EBI is a centre for research and services in Bioinformatics, and is part of European Molecular Biology Laboratory (EMBL The European Molecular Biology Laboratory ( EMBL) is a Molecular biology research institution supported by 20 European countries and Australia as associate member state

Contents

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. Open source is a development methodology which offers practical accessibility to a product's source (goods and knowledge

Most of the software produced and used is written in the language Perl and is based on the BioPerl infrastructure. NOTES FOR EDITORS "Perl" is not an acronym (read the "Name" section below BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for Bioinformatics applications 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 Vertebrate and Genome Annotation (Vega project provides manual curation of Vertebrate Genomes for the scientific community.

Current species

The annotated genomes include most fully sequenced vertebrates and selected model organisms. In classical genetics the genome of a Diploid Organism including Eukarya refers to a full set of chromosomes or genes in a Gamete, thereby Vertebrates are members of the Subphylum Vertebrata, Chordates with backbones or spinal columns The grouping sometimes includes A model organism is a Species that is extensively studied to understand particular biological Phenomena, with the expectation that discoveries made All of them are eukaryotes, there are no prokaryotes. Currently this includes:

Usage

The service is used by molecular biologists and bioinformaticians around the world working with genome data of the above organisms. Year 2007 ( MMVII) was a Common year starting on Monday of the Gregorian calendar in the 21st century. The chicken ( Gallus gallus, sometimes G gallus domesticus) is a domesticated Fowl which is traditionally believed to have descended from is the Japanese word for Pufferfish and is also a Japanese dish prepared from the meat of Pufferfish (normally species of Takifugu, Lagocephalus Tetraodon nigroviridis is one of the Pufferfish known as the Green spotted puffer (the other being Tetraodon fluviatilis) The zebrafish or zebra danio, Danio rerio, a Tropical Freshwater Fish belonging to the minnow family ( Cyprinidae) The Medaka (as it is known in Japanese or Japanese killifish, Oryzias latipes, is a very small Ricefish, popular as an aquarium fish native to The Gasterosteidae are a family of Fish including the sticklebacks. The sea lamprey ( Petromyzon marinus) is a Parasitic Lamprey (a kind of Jawless fish) found on the Atlantic coasts of Caenorhabditis elegans (ˌsiːnoʊræbˈdaɪtɪs ˈɛlɪgænz is a free-living Nematode (roundworm about 1  mm in length which Saccharomyces cerevisiae is a Species of Budding Yeast. It is perhaps the most useful Yeast owing to its use since ancient times Molecular biology is the study of Biology at a molecular level Bioinformatics is the application of information technology to the field of molecular biology 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). Biological databases are libraries of life sciences information collected from scientific experiments published literature high throughput experiment technology and computational analyses

The comparison of organisms (comparative genomics or also intergenomics) with respect to their gene structures and the coded proteins is of special interest. Comparative genomics is the study of the relationship of Genome structure and function across different biological Species or strains. The synteny view can be useful educational material for school classes. In Classical genetics, synteny describes the physical co-localization of genetic loci on the same Chromosome within an individual or Species

See also

External links

Databases supported by Bioinformatic Harvester
NCBI-BLAST | CDD | Ensembl | Entrez | Flybase | Flymine | GFP-cDNA | Genome_browser | GeneCard | Google_Scholar | GoPubMed | HomoloGene | iHOP | IPI | OMIM | Mitocheck | PSORT | PolyMeta | UniProt | SOURCE | SOSUI | RZPD | Sciencenet | STRING | SMART | ZFIN |
The term "sequence analysis" in biology implies subjecting a DNA or Peptide sequence to Sequence alignment, Sequence databases A sequence profiling tool in Bioinformatics is a type of Software that presents information related to a genetic sequence gene name or keyword input In Genetics, a sequence motif is a Nucleotide or amino-acid Sequence pattern that is widespread and has or is conjectured to have a biological The Bioinformatic-Harvester is a bioinformatic meta Search engine at KIT Karlsruhe Institute of Technology for Genes and protein-associated information In Bioinformatics, B asic L ocal A lignment S earch T ool or BLAST, is an Algorithm for comparing primary The Entrez Global Query Cross-Database Search System is a powerful Federated search engine or Web portal that allows users to search many discrete Health sciences FlyBase is an online Bioinformatics Database of the biology and genome of the Model organism Drosophila melanogaster and related Drosophilid The GFP-cDNA project documents the localisation of Proteins to subcellular compartments of the Eukaryotic cell applying Fluorescence microscopy Biological databases are libraries of life sciences information collected from scientific experiments published literature high throughput experiment technology and computational analyses Google Scholar ( GS) is a freely-accessible Web search engine that indexes the full text of Scholarly literature across an array of publishing formats GoPubMed is a knowledge-based search engine for biomedical texts HomoloGene, a tool of the National Center for Biotechnology Information (NCBI is a system for automated detection of homologs (similarity attributable to descent Information Hyperlinked over Proteins (or iHOP) is an online service that provides a gene-guided network to access PubMed abstracts The Mendelian Inheritance in Man project is a Database that catalogues all the known Diseases with a genetic component, and—when possible—links them MitoCheck is an integrated research project which brings together leading European research groups to study systematically the regulation of Mitosis in Human PSORT is a Bioinformatics tool available online at http//psort UniProt is the uni versal prot ein resource a central repository of Protein data created by combining Swiss-Prot, TrEMBL SOSUI is a free online tool that predicts a part of the Secondary structure of proteins from a given Amino acid sequence (AAS "Sciencenet" is an experimental search engine at KIT ( Karlsruhe Institute of Technology - Liebel-Lab for scientific knowledge The Zebrafish Information Network ( ZFIN is an online Biological database of information about the Zebrafish ( Danio rerio)
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