Fig. 6

Appropriate set of alignments. This figure shows how AligNet constructs an appropriate set of alignments considered to obtain a final local alignment. This corresponds to the Step 4 of our aligner. First of all, a maximum score alignment between a pair of clusters is chosen: in this case, this corresponds to the matching between the clusters in Fig. 4. Both clusters are shown in the second row of this figure. The shadowed nodes are the nodes that are not aligned. Next, a maximum score alignment of a pair of clusters with source a cluster centered at a shadowed node is chosen: it turns out to be the one in the second row in Fig. 5 and it is shown in the third row in this figure. Finally, the last alignment to be included in the appropriate set of alignments must be the one with source cluster centered at the remaining shadowed node: this corresponds to the alignment in the last row in Fig. 5 shown in the bottom of this figure. Notice that in the end, that is when we consider the three alignments together, there are four nodes in the source network with inconsistent assignments