title: A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.
abstract: CONCLUSIONS
  Gene Ontology (GO) semantic similarity measures are being used for biological knowledge discovery based on GO annotations by integrating biological information contained in the GO structure into data analyses. To empower users to quickly compute, manipulate and explore these measures, we introduce A-DaGO-Fun (ADaptable Gene Ontology semantic similarity-based Functional analysis). It is a portable software package integrating all known GO information content-based semantic similarity measures and relevant biological applications associated with these measures. A-DaGO-Fun has the advantage not only of handling datasets from the current high-throughput genome-wide applications, but also allowing users to choose the most relevant semantic similarity approach for their biological applications and to adapt a given module to their needs.
  
  
  METHODS
  A-DaGO-Fun is freely available to the research community at http://web.cbio.uct.ac.za/ITGOM/adagofun. It is implemented in Linux using Python under free software (GNU General Public Licence).
  
  
  BACKGROUND
  gmazandu@cbio.uct.ac.za or Nicola.Mulder@uct.ac.za
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa and African Institute for Mathematical Sciences (AIMS), Cape Town, South Africa and Cape Coast, Ghana.
authors.forename: Gaston K
authors.initials: GK
authors.lastname: Mazandu
authors.affiliation: Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa and.
authors.forename: Emile R
authors.initials: ER
authors.lastname: Chimusa
authors.affiliation: Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa and.
authors.forename: Mamana
authors.initials: M
authors.lastname: Mbiyavanga
authors.affiliation: Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa and.
authors.forename: Nicola J
authors.initials: NJ
authors.lastname: Mulder
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D063990:Gene Ontology; D005796:Genes; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods*; D011506:Proteins / Q000235:genetics*; D012660:Semantics; D012984:Software
chemical_list: D011506:Proteins