Gene Ontology Tools

Gene Ontology Tools

• Consortium Tools
• Non-Consortium Tools
• Tools for searching and browsing GO
• Annotation tools
• Tools for gene expression/microarray analysis
• Other tools

Consortium Tools

The tools below are developed within the Gene Ontology Consortium. They continue to be improved and expanded and you can receive support in using these tools by writing to the GO helpdesk.

The tools on this page are free to academics.

AmiGO

Berkeley Bioinformatics and Ontology Project
No abstract available

AmiGO allows you to search for a GO term and view all gene products annotated to it, or search for a gene product and view all its associations. You can also browse the ontologies to view relationships between terms as well as the number of gene products annotated to a given term. AmiGO accesses the GO mySQL database; the browser and documentation are available from the GO database website.

AmiGO is developed and maintained within the GO Consortium.

OBO-Edit

Berkeley Bioinformatics and Ontology Project
No abstract available

OBO-Edit is an open source, platform-independent application for viewing and editing any OBO format ontologies.
OBO-Edit is a graph-based tool; its emphasis on the overall graph structure of an ontology provides a friendly interface for biologists, and makes OBO-Edit excellent for the rapid generation of large ontologies focusing on relationships between relatively simple classes.
OBO-Edit was previously known as DAG-Edit.
OBO-Edit uses the OBO format flat file.
OBO-Edit is developed and maintained within the GO Consortium.

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Non-Consortium Tools

Many tools have been created outside of the consortium for use with the GO ontologies. To see listings of these tools please use the links in the table below.

Tools for searching and browsing GO

Tool to display, browse and search the ontologies and/or annotations.

• CGAP GO Browser
• COBrA
• EP GO Browser
• GeneInfoViz
• GeneOntology at RZPD
• GenNav
• GOblet
• GoFish
• MGI GO Browser
• Ontology Lookup Service
• PANDORA
• QuickGO at EBI
• TAIR Keyword Browser
• Tk-GO

Annotation tools

Tools for annotating genes or gene products using GO

• GeneTools
• GOanna
• GoAnnotator
• GoFigure
• GoPubMed
• GOtcha
• HT-GO-FAT
• InGOt (proprietary)
• JAFA
• Manatee
• PubSearch

Tools for gene expression/microarray analysis

• BiNGO
• CLENCH
• DAVID
• EASE
• eGOn v2.0
• ermineJ
• FatiGO
• FuncAssociate
• FuncExpression
• GARBAN
• GeneMerge
• GFINDer: Genome Function
• GOArray
• GOdist
• GOHyperGAll
• GoMiner and MatchMiner
• GOODIES
• GOstat
• GoSurfer
• GO Term Finder
• GOTM (Gene Ontology Tree Machine)
• GOToolBox
• L2L
• Machaon Clustering and Validation Environment
• MAPPFinder
• NetAffx Gene Ontology Mining Tool
• Onto-Compare
• Onto-Design
• Onto-Express
• Onto-Miner
• Onto-Translate
• OntoGate
• Ontologizer
• Ontology Traverser
• Probe Explorer
• SeqExpress
• SOURCE
• STEM: Short Time-series Expression Miner
• T-Profiler
• THEA
• Avadis - gene expression analysis with GO browser (proprietary)
• Spotfire Gene Ontology Advantage Application (proprietary)

Other tools

• APID
• Blast2GO
• Flash GViewer
• FunSpec
• FuSSiMeG
• Generic GO Term Mapper
• Genes2Diseases
• GO Slim Mapper
• GO Terms Classification Counter
• GOBU
• GOChase
• GOProfiler
• GORetriever
• GOSlimViewer
• TXTGate
• WEGO
• Whatizit

Submit new tools

How to request that your tool be listed on these pages.

From: http://www.geneontology.org/GO.tools.shtml