The main topic of this thesis is functional annotation. Functional annotation consists in associating proteins with biological functions. We explored two aspects of functional annotation. On one hand, we have tested the hypothesis that the order of domains in a protein could play a role in a protein biological function. We have introduced the new notion of sequential nugget of knowledge as an association of a sequence of items with a predetermined target. We have designed and implemented SNK, an algorithm that find such nuggets of knowledge. SNK algorithm has been adapted to fit specific needs expressed by our biologist collaborators. SNK has been successfully used to study a protein family. On the other band, we were interested in biological ontologies and functional hierarchies used by experts to perform functional annotation. Many of these structured and controlled vocabularies exist and express various aspects on the annotation. The mapping of biological ontologies appeared as a need to enable the study of whole set of annotation data for genomics purpose. We have chosen to develop a dedicated method O'Browser, that use specificity of biological ontologies by (i) using a matcher based on homology relationships between proteins annotated with the ontologies, and (ii) introducing the notion of adaptive weighting of matchers. This method has been used for the alignment of two functional hierarchies.
