Ray can output gene ontology profiles using a colored de Bruijn approach.

The graph is colored using EMBL_CDS DNA sequences.
Then, Gene Ontology annotations of those DNA sequence are used
to output a profile.


	EMBL_CDS  <--->  Uniprot  <--->   Gene Ontology




From the manual:

       -gene-ontology OntologyTerms.txt  Annotations.txt
              Provides an ontology and annotations.
              OntologyTerms.txt is fetched from http://geneontology.org
              Annotations.txt is a 2-column file (EMBL_CDS handle	&	gene ontology identifier)
              See Documentation/GeneOntology.txt

The OntologyTerms.txt file is
http://geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo


The annotation file must be derived from Uniprot-GOA
(http://www.ebi.ac.uk/GOA/).




Files created are 

	<RayOutput>/BiologicalAbundances/_GeneOntology/Terms.xml
	<RayOutput>/BiologicalAbundances/_GeneOntology/Terms.tsv


For a script that does everything, see
https://github.com/sebhtml/Paper-Replication-2012