Figure 2.

An example with two networks, A and B. The two tables are the similarity scores with and without preprocessing. The solid lines connecting two proteins in the same network are edges, and bold lines are conserved edges. The arrows across two networks are match-sets. The threshold τ is 50 here. Stage 1 shows the clustering result, which is {{A1, B1}, {A2, B2, B3}, {A3, B4}}. Stage 2 generates seed match-sets. Since here are only two networks, we do not merge any match-set and therefore the seed {A2, B3} is ignored. Stage 3 expands the alignment based on the seed {A2, B2}. There are no alignable pairs after stage 3, so stage 4 is not executed in this example.