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Gene Ontology annotation software tools | Genome annotation

Gene Ontology (GO) is a popular standard in the annotation of gene products and provides information related to genes across all species. Hundreds of GO-focused applications and tools are available and are currently hosted on the NeuroLex site.

Blast2GO
Desktop

Blast2GO

A comprehensive bioinformatics tool for functional annotation of sequences and…

A comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. Blast2GO optimizes…

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GREAT
Web

GREAT

Predicts functions of cis-regulatory regions. Many coding genes are well…

Predicts functions of cis-regulatory regions. Many coding genes are well annotated with their biological functions. Non-coding regions typically lack such annotation. GREAT assigns biological meaning…

BioGPS
Dataset

BioGPS

A centralized gene-annotation portal that enables researchers to access…

A centralized gene-annotation portal that enables researchers to access distributed gene annotation resources. The unique features of BioGPS, compared to those of other gene portals, are its…

Genes2GO
Web

Genes2GO Gene Ontology Matrix Builder

Creates a binary matrix with gene ids as row names and GO IDs/Terms as column…

Creates a binary matrix with gene ids as row names and GO IDs/Terms as column names and is filled with 0s and 1s. If a gene X is annotated with a GO term Y, then the cell XY will contain 1 else a 0.…

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DAVID
Web

DAVID Database for Annotation, Visualization and Integrated Discovery

A web-based online bioinformatics resource that aims to provide tools for the…

A web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. DAVID has been used by researchers from more than 5000…

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BLASTX
Desktop
Web

BLASTX Translated BLAST: blastx

Search protein databases using a translated nucleotide query.

Search protein databases using a translated nucleotide query.

AmiGO
Web

AmiGO

Provides a set of tools for searching and browsing the Gene Ontology (GO)…

Provides a set of tools for searching and browsing the Gene Ontology (GO) database. AMIGO visualizes speciation, duplication and horizontal gene transfer events, sequence alignments and descriptive…

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KOBAS
Web

KOBAS KEGG Orthology Based Annotation System

Its purpose is to identify statistically enriched pathways, diseases, and GO…

Its purpose is to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases.

GO
Web

GO Gene Ontology

A community-based bioinformatics resource that classifies gene product function…

A community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the Gene Ontology (GO) Consortium (GOC) has…

FUNC
Desktop

FUNC

Identifies significant associations between gene sets and ontological…

Identifies significant associations between gene sets and ontological annotations. FUNC allows researchers to correlate their data with gene annotations that are often provided in the form of…

REViGO
Web

REViGO

A web server that can take long lists of Gene Ontology terms and summarize them…

A web server that can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based scatterplots,…

GOrilla
Web

GOrilla Gene Ontology enRIchment anaLysis and visuaLizAtion tool

A web-based application that identifies enriched GO terms in ranked lists of…

A web-based application that identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets. This is particularly useful in many…

GoMapMan
Web

GoMapMan

An open web-accessible resource for gene functional annotations in the plant…

An open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several…

QuickGO
Web

QuickGO

A web-based tool for browsing the GO and all associated GO annotations provided…

A web-based tool for browsing the GO and all associated GO annotations provided by the GOA group. QuickGO has implemented in JavaScript, Ajax and HTML, with all major browsers supported.

NoGOA
Desktop

NoGOA

Applies sparse representation on the gene-term matrix to compute the sparse…

Applies sparse representation on the gene-term matrix to compute the sparse representation coefficients. NoGOA takes advantage of evidence codes attached with annotations and sparse representation to…

RamiGO
Desktop

RamiGO

An R interface to AmiGO that enables visualization of Gene Ontology (GO) trees.…

An R interface to AmiGO that enables visualization of Gene Ontology (GO) trees. Given a list of GO terms, RamiGO uses the AmiGO visualize API to import Graphviz-DOT format files into R, and export…

PEDANT
Dataset

PEDANT

Provides exhaustive automatic analysis of genomic sequences by a large variety…

Provides exhaustive automatic analysis of genomic sequences by a large variety of bioinformatics tools. PEDANT is a database that includes (i) integration with the BioRSTM data retrieval system which…

STRAP
Web

STRAP Software Tool for Rapid Annotation of Proteins

The program automatically annotates a protein list with information that helps…

The program automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques.

Annotare
Desktop

Annotare

A tool for annotating biomedical investigations and resulting data. It is a…

A tool for annotating biomedical investigations and resulting data. It is a stand-alone desktop application that features 1) a set of intuitive editor forms to create and modify annotations, 2)…

GONUTS
Dataset

GONUTS Gene Ontology Normal Usage Tracking System

A community-based browser and usage guide for Gene Ontology (GO) terms and a…

A community-based browser and usage guide for Gene Ontology (GO) terms and a community system for general GO annotation of proteins.

GOProfiler
Web

GOProfiler

Provides a summary of GO annotations available for each species. The user…

Provides a summary of GO annotations available for each species. The user provides a taxon id and GOProfiler displays the number of GO associations and the number of annotated proteins for that…

GOSlimViewer
Web

GOSlimViewer

It is used to provide a high level summary of functions for a dataset. The…

It is used to provide a high level summary of functions for a dataset. The output can be charted in Excel to obtain publication quality figures. Note that records without annotation are not analyzed…

goSTAG
Desktop

goSTAG

Uses Gene Ontology (GO) subtrees to tag and annotate genes within a set. goSTAG…

Uses Gene Ontology (GO) subtrees to tag and annotate genes within a set. goSTAG visualizes the similarities between the overrepresentation of differentially expressed genes (DEGs) by clustering the…

NaviGO
Web

NaviGO

Allows interactive visualization and retrieval of Gene Ontology (GO) terms and…

Allows interactive visualization and retrieval of Gene Ontology (GO) terms and genes. NaviGO analyzes functional similarity and associations of GO terms and genes. It constructs similarity matrices…

Metastudent
Desktop

Metastudent

Allows users to predict Gene Ontology (GO) terms from the Molecular Function…

Allows users to predict Gene Ontology (GO) terms from the Molecular Function Ontology (MFO) and Biological Process Ontology (BPO). Metastudent represents a method that compares predicted and…

NoisyGOA
Desktop

NoisyGOA Noisy GO Annotations

Removes noisy annotations. NoisyGOA firstly computes the taxonomic similarity…

Removes noisy annotations. NoisyGOA firstly computes the taxonomic similarity between two ontological terms using the ontology structure, and the semantic similarity between two groups of terms…

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Interpro2GO
Desktop

Interpro2GO

Classifies sequences into protein families and predicts the presence of…

Classifies sequences into protein families and predicts the presence of important domains and sites. InterPro is an integrated resource of protein families, domains and sites which are combined from…

GRYFUN
Web

GRYFUN

Generates Gene Ontology annotation graphs for protein sets and their associated…

Generates Gene Ontology annotation graphs for protein sets and their associated statistics from simple frequencies to enrichment values and information content based metrics. GRYFUN is a freely…

PiNGO
Desktop

PiNGO

A Java-based tool to easily find unknown genes in a network that are…

A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a…

CompGO
Desktop

CompGO

A bioinformatics tool for identifying Differentially Enriched Gene Ontologies,…

A bioinformatics tool for identifying Differentially Enriched Gene Ontologies, called DiEGOs, and pathways, through the use of a z-score derivation of log odds ratios, and visualizing these…

GoFish
Desktop

GoFish

This program allows the user to select a subset of Gene Ontology (GO)…

This program allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes.

NeuroLex.org
Dataset

NeuroLex.org

A freely editable semantic wiki for community-based curation of the terms used…

A freely editable semantic wiki for community-based curation of the terms used in Neuroscience.

IsoFunc
Dataset

IsoFunc

A tool for assigning function to the human protein-coding splice variants…

A tool for assigning function to the human protein-coding splice variants (PCSVs). Most of previous studies have been focused only on the gene-centric functional annotation but now evidence is…

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WTFgenes
Desktop
Web

WTFgenes What’s The Function of these genes?

Interprets experimentally-identified lists of genes. WTFgenes uses…

Interprets experimentally-identified lists of genes. WTFgenes uses hypergeometric and model-based approaches. It permits to know what is the function of different genes thanks to Bayesian Term…

GOsummaries
Desktop

GOsummaries

Visualizes the GO (Gene Ontology) enrichment results as concise word clouds…

Visualizes the GO (Gene Ontology) enrichment results as concise word clouds that can be combined together if the number of gene lists is larger. By showing the annotations as word clouds and…

IT-GOM
Web

IT-GOM Integrated Tool for IC-based GO Semantic Similarity Measures

This engine provides the information content (IC) of GO terms, semantic…

This engine provides the information content (IC) of GO terms, semantic similarity between GO terms and GO-based protein functional similarity scores. The specificity of GO terms and the similarity…

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GOstats
Desktop

GOstats

Tests Gene Ontology (GO) terms for over or under-representation using either a…

Tests Gene Ontology (GO) terms for over or under-representation using either a classical hypergeometric test or a conditional hypergeometric that uses the relationships among GO terms to decorrelate…

CluePedia
Desktop

CluePedia

A search tool for new markers potentially associated to pathways. CluePedia…

A search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data. Genes, proteins and miRNAs linked based…

TXTGate
Web

TXTGate

Combines literature indices of selected public biological resources in a…

Combines literature indices of selected public biological resources in a flexible text-mining system designed towards the analysis of groups of genes. TXTGate is a platform that offers multiple…

GenGO
Web

GenGO GENerative GO analysis

Accommodates noise and errors in the selected gene set and Gene Ontology (GO).…

Accommodates noise and errors in the selected gene set and Gene Ontology (GO). GenGO analyses the GO hierarchy for yeast and humans. This platform is effective in minimizing false positives while at…

GOblet
Web

GOblet

Allows to navigate pathway knowledge and provides bioinformatics tools for the…

Allows to navigate pathway knowledge and provides bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge. Reactome is a manually curated and peer-reviewed…

AMEN
Desktop

AMEN Annotation Mapping Expression and Network

Enables biological and medical researchers with basic bioinformatics training…

Enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein -protein interaction (PPI), expression profiling…

GOTA
Web

GOTA GO Term Annotation

A Gene Ontology (GO) term annotator for biomedical literature. The proposed…

A Gene Ontology (GO) term annotator for biomedical literature. The proposed approach makes use only of information that is readily available from public repositories and it is easily expandable to…

BD-Func
Desktop

BD-Func BiDirectional FUNCtional enrichment

Calculates functional enrichment by comparing lists of pre-defined genes that…

Calculates functional enrichment by comparing lists of pre-defined genes that are known to be activated versus inhibited in a pathway or by a regulatory molecule. BD-Func predicts cell line…

GoGrapher
Desktop

GoGrapher

Contains common routines for graph operation and analysis, for instance,…

Contains common routines for graph operation and analysis, for instance, creation of graphs, finding shortest paths, extracting minimum spanning trees, and graph topology analysis. GOGrapher is a…

Gene Class
Web

Gene Class

Provides an interactive visualization of functional annotation of two lists of…

Provides an interactive visualization of functional annotation of two lists of Serial analysis of gene expression (SAGE) tags in the corresponding Gene Ontology (GO) category. Gene Class provides…

GOpro
Desktop

GOpro

Finds the most characteristic gene ontology terms for groups of human genes.…

Finds the most characteristic gene ontology terms for groups of human genes. Determine groups of genes and find their most characteristic gene ontology (GO) term.

GOTreePlus
Desktop

GOTreePlus

An interactive gene ontology (GO) browser that superimposes annotation…

An interactive gene ontology (GO) browser that superimposes annotation information over GO structures. GOTreePlus can facilitate the identification of important GO terms through interactive…

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GOstat
Web

GOstat

Find statistically overrepresented GO terms within a group of genes. This…

Find statistically overrepresented GO terms within a group of genes. This program automatically obtains the GO annotations from a database and generates statistics of which annotations are…

OntoVisT
Web

OntoVisT

This application is designed for interactive visualization of any ontological…

This application is designed for interactive visualization of any ontological hierarchy for a specific node of interest, up to the chosen level of children and/or ancestor.

GOParGenPy
Desktop

GOParGenPy

A platform independent software tool to generate the binary data matrix showing…

A platform independent software tool to generate the binary data matrix showing the GO class membership, including parental classes, of a set of GO annotated genes. GOParGenPy is at least an order of…

GOAtools
Desktop

GOAtools Gene Ontology Association tools

Contains a library to process over- and under-representation of certain gene…

Contains a library to process over- and under-representation of certain gene ontology (GO) terms, based on Fisher's exact test. GOAtools is a python package that process the obo-formatted file…

GO MWU
Desktop

GO MWU

Provides methods to analysis gene expression. In contrast to most other…

Provides methods to analysis gene expression. In contrast to most other "GO enrichment analysis" methods, GO MWU does not look for Gene Ontology (GO) categories enriched within a list of…

godef
Desktop

godef

Finds gene ontology (GO) terms by definition and returns matching terms. The…

Finds gene ontology (GO) terms by definition and returns matching terms. The input for godef is read from the installed GO database. The ontology term output can be written to screen, to file, or…

GOLEM
Desktop

GOLEM Gene Ontology Local Exploration Map

Provides dynamic graph-based visualization of the Gene Ontology (GO) hierarchy.…

Provides dynamic graph-based visualization of the Gene Ontology (GO) hierarchy. GOLEM provides a dynamically expandable graph display of a local portion of GO. This method also purposes gene set…

GObar
Web

GObar

Allows to analyze some large gene lists. GObar allows visualization and…

Allows to analyze some large gene lists. GObar allows visualization and identification of pathways. The tool is able to identify sub-groups of genes that cannot be explained by chance alone. It…

SimCT
Web

SimCT Similarity Clustering Tree

Allows to graphically display the relationships between biological objects…

Allows to graphically display the relationships between biological objects (e.g. genes or proteins) based on their annotations to a biomedical ontology. The result is presented as a tree of these…

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