Figure 4

Coverage completion. Comparison of the results of Proteinortho with different thresholds of the normalized algebraic connectivity with the COG-database and OrthoMCL for a dataset consisting of 16 randomly chosen bacterial proteomes. The vertical dashed line marks the transition from clusters containing mainly a single ortholog from each species to sets including co-orthologs. The COG-database reports many large groups which often include co-orthologous proteins. OrthoMCL and Proteinortho focus on highly connected subsets in order to find orthologous sets and thus split those groups. Thereby, Proteinortho's clustering algorithm becomes more stringent with increasing values of in splitting in particular large groups. While these groups are left intact for , thresholds of 0.5 and higher drastically reduce the fraction of included co-orthologs.