rama balakrishnan
DESCRIPTION
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) - PowerPoint PPT PresentationTRANSCRIPT
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Rama Balakrishnan
AmiGO Tutorial
Saccharomyces Genome Database (SGD)Stanford University
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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
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AmiGOhttp://www.godatabase.org
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Basic Search
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More on term search results
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Term Details Page
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Gene Product Details and Annotations
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Browsing the Ontologies
Is_a relationship
Part_of relationship
Leaf node or no children
Node has been opened, can be clicked to closeNode 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.
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Annotations associated with a termAnnotation data are from the gene_associations file submitted by the annotating groups
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Advanced search
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Filters
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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)
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GOst can also be accessed from the annotations section
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AmiGO Help