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Rama Balakrishnan

Rama Balakrishnan. AmiGO Tutorial. Saccharomyces Genome Database (SGD) Stanford University. What is AmiGO?. Web application that reads from the GO Database (mySQL) Allows to browse the ontologies view annotations from various species compare sequences using BLAST (GOst)

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Rama Balakrishnan

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  1. Rama Balakrishnan AmiGO Tutorial Saccharomyces Genome Database (SGD) Stanford University

  2. What is AmiGO? • Web application that reads from the GO Database (mySQL) • Allows to • browse the ontologies • view annotations from various species • compare sequences using BLAST (GOst) • Ontologies are loaded into the database from the gene_ontology.obo file • Annotations are loaded from the gene_association files submitted by the various annotating groups • Only ‘Non-IEA’ annotations are loaded

  3. AmiGOhttp://www.godatabase.org

  4. Basic Search

  5. More on term search results

  6. Term Details Page

  7. Gene Product Details and Annotations

  8. Node has children, can be clicked to view children Node has been opened, can be clicked to close Leaf node or no children Is_a relationship Part_of relationship pie chart summary of the numbers of gene products associated to any immediate descendants of this term in the tree. Browsing the Ontologies

  9. Annotations associated with a term Annotation data are from the gene_associations file submitted by the annotatinggroups

  10. Advanced search

  11. Filters

  12. GOST-Gene Ontology blaST • Blast a protein sequence against all gene products that have a GO annotation • Can be accessed from the AmiGO Home page (front page)

  13. GOst can also be accessed from the annotations section

  14. AmiGO Help

  15. Contact us • We welcome your input • Please send suggestions, bugs to us • gohelp@geneontology.org

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