GOtcha 200812 – Prediction of Gene Function by Application of Gene Ontology

GOtcha 200812

:: 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

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GOtcha

:: 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)

gowinda 1.12 – Gene Ontology Term Enrichment for Genome Wide Association Studies

gowinda 1.12

:: DESCRIPTION

Gowinda is a multi-threaded Java application that allows an unbiased analysis of gene set enrichment for Genome Wide Association Studies.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java
  • Python

:: DOWNLOAD

 gowinda

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Aug 1;28(15):2084-5. doi: 10.1093/bioinformatics/bts315. Epub 2012 May 26.
Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies.
Kofler R1, Schlötterer C.

MANGO – Prediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology)

MANGO

:: DESCRIPTION

MANGO is a server for predicting functional class of a protein. It predict function according to GO categories. The method is developed on protein in UNIPROT database whoes function have been assigned manually according to GO criteria.

::DEVELOPER

Dr. G P S Raghava,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Raghava, G. P. S. (2006)
MANGO: prediction of Genome Ontology (GO) class of a protein from its amino acid and dipeptide composition using nearest neighbor approach.
CASP7: 93

GOfact 20051017 – An Integrated Strategy for Functional Analysis in Large-scale Proteomic Research by Gene Ontology

GOfact 20051017

:: DESCRIPTION

GOfact is developed to identify the functional distribution and the significantly enriched functional categories of the proteomic expression profile. It would be helpful for understanding the overall functions of these identified proteins and supply the fundamental information for further bioinformatics exploration.

::DEVELOPER

The State Key Laboratory of Proteomics, Beijing Proteome Research Center (BPRC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • Perl

:: DOWNLOAD

  GOfact

:: MORE INFORMATION

Citation

Li Dong, Li Jian-Qi, Ouyang Shu-Guang, Wang Jian, Xu Xiaojie, Zhu Yun-Ping, He Fu-Chu.
An Integrated Strategy for Functional Analysis in Large-scale Proteomic Research by Gene Ontology.
Biochemistry and Biophysics 2005,32(11):1026-1029

GOExtender 20151030 – Extending Gene Ontology with Gene Association Networks

GOExtender 20151030

:: DESCRIPTION

GOExtender is a new algorithm to efficiently identify all the connected gene pairs labeled by the same parent Gene Ontology (GO) terms.

::DEVELOPER

Jiajie Peng (jiajiepeng@hit.edu.cn), Chen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • JRE

:: DOWNLOAD

 GOExtender

:: MORE INFORMATION

Citation

Extending Gene Ontology with Gene Association Networks.
Peng J, Wang T, Wang J, Wang Y, Chen J.
Bioinformatics. 2015 Dec 7. pii: btv712.

A-DaGO-Fun / DaGO-Fun – Gene Ontology Semantic Similarity based Functional Analysis

A-DaGO-Fun / DaGO-Fun

:: DESCRIPTION

A-DaGO-Fun is a python library that provides a comprehensive and customized set of Gene Ontology (GO) based functional analysis tools that exploit the biological knowledge that GO offers in describing genes or groups of genes through the use of GO semantic similarity measures for biological knowledge discovery.

The DaGO-Fun tool is a an integrated set of GO-based functional analysis tools incorporating the large amounts of biological knowledge that GO offers in describing genes or groups of genes.

::DEVELOPER

The UCT Computational Biology Group (CBIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

A-DaGO-Fun: An adaptable Gene Ontology semantic similarity based functional analysis tool.
Mazandu GK, Chimusa ER, Mbiyavanga M, Mulder NJ.
Bioinformatics. 2015 Oct 17. pii: btv590.

DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures.
Mazandu GK, Mulder NJ.
BMC Bioinformatics. 2013 Sep 25;14:284. doi: 10.1186/1471-2105-14-284.

GOTreePlus 20080131 – Interactive Gene Ontology Browser

GOTreePlus 20080131

:: DESCRIPTION

GOTreePlus is an interactive gene ontology visualization tool that can superimpose annotation information over gene ontology structures. GOTreePlus can facilitate the identification of important GO terms while visualizing them in the gene ontology structure. The interactive pie chart summary for a selected gene ontology term provides users with a succinct overview of their experimental results.

::DEVELOPER

GOTreePlus Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET Framework 2.0

:: DOWNLOAD

 GOTreePlus

:: MORE INFORMATION

Citation

Bongshin Lee, Kristy Brown, Yetrib Hathout, and Jinwook Seo,
GOTreePlus: An Interactive Gene Ontology Browser,”
Bioinformatics (2008) 24 (7): 1026-1028.

Ontologizer 2.1 – Analysis and Visualization of High-Throughput Biological Data Using Gene Ontology

Ontologizer 2.1

:: DESCRIPTION

Ontologizer is a Java webstart application for GO term enrichment analysis that provides browsing and graph visualization capabilities. The Ontologizer allows users to analyze data with the standard Fisher exact test and also the parent-child method and topology methods.

::DEVELOPER

The Computational Biology @ Charité Berlin at the Institute for Medical Genetics and Human Genetics at Charité-Universitätsmedizin Berlin

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

  Ontologizer

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jul 15;24(14):1650-1. Epub 2008 May 29.
Ontologizer 2.0–a multifunctional tool for GO term enrichment analysis and data exploration.
Bauer S, Grossmann S, Vingron M, Robinson PN.

GOseq 1.20.0 – Performing Gene Ontology (GO) based tests on RNA-seq data

GOseq 1.20.0

:: DESCRIPTION

GOseq is an R library for performing Gene Ontology (GO) and other category based tests on RNA-seq data, which corrects for selection bias.

::DEVELOPER

WEHI Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GOseq

:: MORE INFORMATION

Citation

Gene ontology analysis for RNA-seq: accounting for selection bias
Matthew D. Young, Matthew J. Wakefield, Gordon K. Smyth, Alicia Oshlack
Genome Biology 2010, 11:R14 (4 February 2010)

PathwaysWeb 2.0 – Gene Pathways API with Directional Interactions, Expanded Gene Ontology, and Versioning

PathwaysWeb 2.0

:: DESCRIPTION

PathwaysWeb provides publicly available information on genes, biological pathways, Gene Ontology terms, gene gene interaction networks with interaction directionality, and links to related PubMed documents.

::DEVELOPER

PathwaysWeb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PathwaysWeb: A Gene Pathways API with Directional Interactions, Expanded Gene Ontology, and Versioning.
Melott JM, Weinstein JN, Broom BM.
Bioinformatics. 2015 Sep 23. pii: btv554.