Figure 3

Results of comparisons between porthoDom or proteinortho against the OrthoDB database. Different parameters are used for the domain content similarity step of porthoDom and the default parameters of proteinortho are used for both methods. The parameters are: a domain content similarity cut-off of 0.5, a domain content similarity of O1 corresponding to single domain comparisons, or O2 corresponding to the comparison of pairs of domains, and an option collapsing or not of tandem domain repeats. The different parameters have little influence on porthoDom due to the robustness of the domain content similarity method.