Difference between revisions of "AmiGO Manual: Overview"

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* <a href="help-term_search.shtml" title="search for a GO terms">search for GO terms</a> and view the genes or gene products they are annotated to  
 
* <a href="help-term_search.shtml" title="search for a GO terms">search for GO terms</a> and view the genes or gene products they are annotated to  
 
* <a href="help-browse.shtml" title="browse the ontology">browse the GO ontology</a> and view terms  
 
* <a href="help-browse.shtml" title="browse the ontology">browse the GO ontology</a> and view terms  
* slimmer: TODO
+
* the [[AmiGO_Manual:_Slimmer slimmer tool]] can be used to map the granular annotations of the query set of genes to one or more high-level
 
* term enrichment: TODO
 
* term enrichment: TODO
 
* GOOSE: TODO
 
* GOOSE: TODO

Revision as of 11:39, 5 March 2009

Introduction

AmiGO is the official web-based set tools for searching and browsing the Gene Ontology database, which consists of a controlled vocabulary of terms covering biological concepts, and a large number of genes or gene products whose attributes have been annotated using GO terms.

It can be accessed online at the main installation or deployed locally.

To learn more about what the Gene Ontology is and what it does, please read the introductory documentation.

What can I do using AmiGO?

  • <a href="help-gp_search.shtml" title="search for a gene or gene product">search for a gene or gene product</a>, or a list of gene or gene products, and view the GO term associations
  • perform a <a href="help-gost_query.shtml" title="search by sequence using BLAST">sequence identity BLAST search</a> and view the GO term associations for the genes or proteins returned
  • <a href="help-term_search.shtml" title="search for a GO terms">search for GO terms</a> and view the genes or gene products they are annotated to
  • <a href="help-browse.shtml" title="browse the ontology">browse the GO ontology</a> and view terms
  • the AmiGO_Manual:_Slimmer slimmer tool can be used to map the granular annotations of the query set of genes to one or more high-level
  • term enrichment: TODO
  • GOOSE: TODO

Availability

AmiGO is an open source software project and can be downloaded and installed as part of the go-dev CVS repository from the Gene Ontology SourceForge.net page.

For full installation instructions, please see the AmiGO_Manual:_Installation wiki pages.

Browser Compatibility

AmiGO is compatible with most modern operating system/browser combinations with good CSS support, including:

  • Firefox on Linux, Windows, and Mac OS X.
  • Mozilla/Netscape 6 on Linux, Windows, and Mac OS X.
  • IE on Windows, but NOT on Mac OS X. IE on Mac OS X does support CSS standards.
  • Safari on Mac OS X.
  • Konqueror on Linux.
  • Opera on Linux, Windows, and Mac OS X.

In order to use all of the functionality available in this version of AmiGO, we recommend that cookies are allowed and JavaScript is turned on. The Main Window

The HTML page you view may vary slightly in details.

Components

AmiGO is made up of several interacting programs that work together to create a coherent whole.

Main components

The most used components

AmiGO's major components are the ones that are listed at the top of ever page; these are the ones where your work will usually begin.

Pages from the main components

Other Components

AmiGO's other components are those that have specialized output in result of some kind of action.