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

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Presentation on theme: "Rama Balakrishnan AmiGO Tutorial Saccharomyces Genome Database (SGD) Stanford University."— Presentation transcript:

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 AmiGO

4 Basic Search

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6 More on term search results

7 Term Details Page

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9 Gene Product Details and Annotations

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

11 Annotations associated with a term Annotation data are from the gene_associations file submitted by the annotating groups

12 Advanced search

13 Filters

14 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)

15 GOst can also be accessed from the annotations section

16 AmiGO Help

17 Contact us We welcome your input Please send suggestions, bugs to us


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