Ensembl genome


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Ensembl genome

  1. 1. Ensembl Genomes extending Ensembl across the taxonomic space Amer Talal Wazwaz [email_address] [email_address] 21/3/2011
  2. 2. Ensembl Genomes http :// www . ensemblgenomes . org / <ul><li>since April 2009 </li></ul><ul><li>An extension of ensembl </li></ul><ul><li>since July2000 </li></ul><ul><li>Developed jointly by </li></ul><ul><li>EBI and Wellcome </li></ul><ul><li>Trust </li></ul><ul><li>Sanger </li></ul><ul><li>Institute </li></ul>
  3. 3. Introduction   <ul><li>What is Ensembl Genomes </li></ul><ul><li>New portal offering integrated access to genome-scale data for non-vertebrate species, developed using the Ensembl genome annotation and visualization platform </li></ul>Consists of five sub-portals (for bacteria , protists , fungi , plants and invertebrate metazoa ) designed to complement the availability of vertebrate genomes in Ensembl.
  4. 4. Ensembl Genomes http :// www . ensemblgenomes . org / <ul><li>Each site contains data for selected species from their domain, chosen for their scientific interest. </li></ul><ul><li>Information is available about each species, including the assembly version and annotation methods used, the overall composition of the genome </li></ul>
  5. 5. Statement of Need In response to the need of creating annotated genome databases To represent the best annotation for every genome THRO UGH Working with all sections of the relevant scientific community The browser offers a number of views of locations in the genome, genes, and specific transcripts location view for a region of a chromosome gene view transcript view
  6. 6. Statement of Need  Main functionality <ul><li>Portals offer access to a graphical view of each genome, using the Ensembl genome browser software. </li></ul><ul><li>Graphical </li></ul><ul><li>Karyotype </li></ul><ul><li>Views </li></ul>Nonbacterial Bacterial
  7. 7. Data Nature of the DB ENA / GenBank / DDBJ Gramene TAIR NASC IGGP ENA / GenBank / DDBJ Saccharomyces Genome Database GeneDB Central Aspergillus Data Repository ENA / GenBank / DDBJ FlyBase WormBase VectorBase Drosophila Population Genome Project ENA / GenBank / DDBJ Regulon DB ENA / GenBank / DDBJ PlasmoDB EBI staff active participants in their primary annotation Collaborators to build Ensembl databases Importing canonical data from an authority for a given species Records previously submitted to the ENA / GenBank / DDBJ public nucleotide archives Supplemented by protein functional annotation from UniProtKB
  8. 8. Methods of Data Retrieval <ul><li>Ensembl Genomes data is available through </li></ul>BioMart data warehousing system ( API ) Perl These interfaces are supported by a number of relational ( MySQL ) (RDBMS) database schemas “ efficient high-level access “ That run as a server providing multi-user access to Core databases describing sequence, features and stable identifiers Additional databases for other certain types of data
  9. 9. Added Tools <ul><li>Assembly Converter </li></ul><ul><li>Map your data to the current assembly. </li></ul><ul><li>ID History Converter </li></ul><ul><li>Convert a set of Ensembl IDs from </li></ul><ul><li>a previous release into their current equivalents. </li></ul><ul><li>Variant Effect Predictor </li></ul><ul><li>(Formerly SNP Effect Predictor) </li></ul><ul><li>This tool takes a list of variant positions and alleles, and predicts the effects of each of these on any overlapping features (transcripts, regulatory features) annotated in Ensembl. </li></ul>
  10. 10. Short Tutorial <ul><li>Search for a certain gene </li></ul><ul><li>We will get a list of the matched gene in different species </li></ul><ul><li>At the top of the page there are 3 tabs </li></ul><ul><li>Location </li></ul><ul><li>Gene </li></ul><ul><li>Protein </li></ul><ul><li>Graphical alignment of gene of interest </li></ul>
  11. 11. Short Tutorial <ul><li>The gene of interest highlighted against the genomic contig </li></ul><ul><li>Adjacent genes on either </li></ul><ul><li>sides are shown </li></ul>
  12. 12. Short Tutorial <ul><li>Genomic location page </li></ul><ul><li>Graphical representation of protein </li></ul>
  13. 13. Short Tutorial <ul><li>Useful information at the </li></ul><ul><li>sub-gene summary page tabs </li></ul>
  14. 14. Thank You <ul><li>Questions </li></ul>