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new gene ontology software

Bernard jacq at ibdm.univ-mrs.fr
Mon Feb 28 08:35:46 EST 2005

Dear colleagues,

 This short mail to inform the  community of people interested in the 
development and use of biological software of the availability of 
GOToolBox, a series of programs using Gene ontology that we published 
recently in Genome biology 

 The programs from GOToolBox are directly accessible through a Web 
site described in the article.
 They can be useful to analyse groups of genes derived from 
microarrays,Chromatin-Immunoprecipitations, from the analysis of 
protein-protein, protein_DNA and/or genetic networks, ....
 They ca therefore be of potential utility for functional annotations 
of chromosomes.

 GOToolBox performs five main tasks:

 - gene dataset creation,
 - selection and fitting of GO terms at a given ontology level (GO-Diet),
 - statistical analysis of GO terms associated with gene sets 
(GO-Stats) in order to find over- or under-represented terms,
 - GO-based gene clustering (GO-Proxy) allowing to find sub-groups of 
functionnally related genes within a gene set,
 - gene retrieval based on GO annotation similarity (GO-Family) in 
one or several species.

 Other developments are presently on their way.
 At the moment, GOToolBox supports analyses of GO terms for six species :
Yeast (Sc), Arabidopsis, Drosophila, nematode, mouse and humans.

 For the authors,

 David Martin and Bernard Jacq

Bernard Jacq
Parc Scientifique de luminy
13288 Marseille Cedex 9

tel (33) 04 91 82 94 25
fax (33) 04 91 82 06 82

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