I need to propagate a set of predicted GO terms to the root of the Gene Ontology Directed Acyclic Graph (DAG) and to calculate recall. Any recommendation for a tool free for academics?
Do you mean you want the actual path the GO takes to reach the root?
No, I didn’t mean that.
I will try to be more specific: we predicted GO terms describing protein functions and then compare the predictions with the original functions defined by GO database. All the GO term nodes existing in the paths of the predicted GO terms toward the root are considered matches. The recall is defined as the fraction of matches between the annotated and the predicted functions among the original function annotations.