Ensembl

Ensembl is a bioinformatics research project, which aims " to develop software that automatically creates entries for eukaryotic genome and cares ." It is operated in collaboration with the Wellcome Trust Sanger Institute and the European Bioinformatics Institute (EBI ), to an outpost of the European Molecular Biology Laboratory ( EMBL). All data and software produced in this project can be viewed and used by anyone. The uploading and also the downloading of data is possible. Most of the software is based on Perl and BioPerl infrastructure.

The following genomes of vertebrates and model organisms can be viewed and searched:

  • Chordates Mammals: human (Homo sapiens), chimpanzee (Pan troglodytes), rhesus monkey (Macaca mulatta), house mouse (Mus musculus), brown rat (Rattus norvegicus), domestic dog ( Canis familiaris), cattle (Bos taurus), African elephant ( Loxodonta africana), opossum ( Monodelphis domestica), Brown -breasted Hedgehog (Erinaceus europaeus), domestic horse (Equus caballus )
  • Birds: Chicken (Gallus gallus)
  • Fish: zebra fish (Danio rerio), fugu ( Takifugu rubripes ), green puffer ( Tetraodon nigroviridis )
  • Sea Squirts: Schlauchascidie ( Ciona intestinalis ), Ciona savignyi
  • Invertebrates Insects: the fruit fly Drosophila melanogaster, the mosquito Anopheles gambiae, honey bee ( Apis mellifera)
  • Nematode Caenorhabditis elegans
  • Yeast: Brewer's yeast (Saccharomyces cerevisiae)

Data display

On the input side of the individual species, the user first finds statistics, general information about the genome and news.

The genetic map can be accessed either by simply clicking on a chromosome segment or by manual input of genetic markers. On the side of four sub- sections are:

  • The entire chromosome with highlighted neck, which is considered in detail
  • Overview: an overview of possible Syntänien (the presence of chromosomal regions with the same genes in the same order in different species ) genes and markers in the selected region
  • Detailed View: genes, mRNA, proteins, etc. can be seen here
  • Base Pair View: Shows the nucleotide with its three possible reading frames and the resulting amino acid sequences

Search functions

  • Keyword search: use "Search Ensembl ' can search the genomes provided the user eg for genes that marker names, proteins, diseases or syndromes.
  • BLAST: the BLAST search function makes it possible to compare a given nucleotide or protein sequence with the database.
  • Export View: View Export finds gene regions based on the input of coordinates.
  • Data mining ( BioMart ): This tool allows precise through various filter settings search for genetic regions.
Frederick Sanger African bush elephant Bioinformatic Harvester Entrez GFP-cDNA Google Scholar GoPubMed HomoloGene Information Hyperlinked over Proteins Mouse Genome Informatics Mitocheck PSORT UniProt SOSUI STRING
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