Among features relevant for protein function assignment, orthology relations and domain architecture are both important. A systematic, large-scale study of domain architecture conservation in orthologous vs paralogous proteins has so far been lacking. We attempt an analysis of this type, using the Inparanoid framework as a basis. As a spin-off from this project, we've also begun a comparison of different strategies for handling false positive homology assignments as a result of sequences having very biased residue composition.
