1 / 17

Comprehensive Guide to AmiGO: Exploring the Saccharomyces Genome Database

Discover AmiGO, a powerful web application developed at Stanford University that provides access to the Gene Ontology (GO) database. With AmiGO, users can browse ontologies, view annotations from various species, and compare gene sequences using BLAST (GOst). This tutorial will guide you through the functionalities, including ontology browsing, advanced search filters, and interpretation of annotation data. Whether you're a researcher or a student, learn how to leverage AmiGO for your genomic studies effectively.

penda
Télécharger la présentation

Comprehensive Guide to AmiGO: Exploring the Saccharomyces Genome Database

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

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. 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

More Related