:: DESCRIPTION
GOGO is an improved algorithm to measure the semantic similarity of gene ontology terms
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhao C, Wang Z.
GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms.
Sci Rep. 2018 Oct 10;8(1):15107. doi: 10.1038/s41598-018-33219-y. PMID: 30305653; PMCID: PMC6180005.
:: DESCRIPTION
CateGOrizer, previously known as “GO Terms Classifications Counter”, is a free web tool for users to batch analyze GO term data sets in terms of GO classes they represent.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Zhi-Liang Hu, Jie Bao and James M. Reecy (2008)
“CateGOrizer: A Web-Based Program to Batch Analyze Gene Ontology Classification Categories“.
Online J Bioinform. 9 (2):108-112.
:: DESCRIPTION
Csbl.go is an R package for computing semantic similarity between genes using Gene Ontology annotation and for clustering genes based on the similarity measures. The package also includes GO enrichment analysis functionality.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fast Gene Ontology based clustering for microarray experiments
Kristian Ovaska, Marko Laakso and Sampsa Hautaniemi
BioData Mining 2008, 1:11
:: DESCRIPTION
Argot2 (Annotation Retrieval of Genel Ontology Terms) is able to quickly process thousands of sequences for functional inference. The tool exploits a combined approach based on the clustering process of GO terms dependent on their semantic similarities and a weighting scheme which assesses retrieved hits sharing a certain degree of biological features with the sequence to annotate.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S14. doi: 10.1186/1471-2105-13-S4-S14.
Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.
Falda M1, Toppo S, Pescarolo A, Lavezzo E, Di Camillo B, Facchinetti A, Cilia E, Velasco R, Fontana P.
:: DESCRIPTION
GOssTo is a Java based semantic similarity calculator. Bundled in the software are the well-known Resnik, Lin, Jian, simUI, simGRASM similarity measures. It features powerful extension capabilities allowing the user to add as many similarity measures as needed.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Mar 22. [Epub ahead of print]
GOssTo: a user-friendly stand-alone and web tool for calculating semantic similarities on the Gene Ontology.
Caniza H1, Romero AE, Heron S, Yang H, Devoto A, Frasca M, Mesiti M, Valentini G, Paccanaro A.
:: DESCRIPTION
GOtcha uses sequence similarity searches to associate GO terms with your sequence. These are ranked by probability and displayed graphically on a subtree of Gene Ontology.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Martin,DMA, Berriman, M and Barton, GJ (2004),
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes,
BMC Bioinformatics, 5:178 (18 November 2004)
:: DESCRIPTION
GOrilla is 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 typical cases where genomic data may be naturally represented as a ranked list of genes (e.g. by level of expression or of differential expression).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson and Zohar Yakhini.
“GOrilla: A Tool For Discovery And Visualization of Enriched GO Terms in Ranked Gene Lists“,
BMC Bioinformatics 2009, 10:48.
:: DESCRIPTION
GOMEP Predicts Missing Enzymes using functional coherence scores of Gene Ontology (GO) terms
::DEVELOPER
Kihara Bioinformatics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sci Rep. 2016 Aug 24;6:31725. doi: 10.1038/srep31725.
Missing gene identification using functional coherence scores.
Chitale M, Khan IK, Kihara D
:: DESCRIPTION
NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes.
::DEVELOPER
Kihara Bioinformatics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.
Wei Q, Khan IK, Ding Z, Yerneni S, Kihara D.
BMC Bioinformatics. 2017 Mar 20;18(1):177. doi: 10.1186/s12859-017-1600-5.
:: DESCRIPTION
PhyloPFP is a phylogenomics based protein function prediction server
::DEVELOPER
Kihara Bioinformatics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2019 Mar 1;35(5):753-759. doi: 10.1093/bioinformatics/bty704.
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences.
Jain A, Kihara D.