Figure 1

Outline of a pairwise partial gene order alignment of two genomes. This figure depicts all required steps to compute a pairwise gene order alignment of two genomes. Step 1 involves the pairwise comparison of all contiguous sequence regions of two species. The alignment matrix is shown for one pairwise comparison of two partially ordered gene sets: A_{1,2,4,5,6,7,9,10,11,12} and B_{1,2,3,4a,5a,8,4b,5b,10,11,12}. The gene indices express homology relations (e.g. A₁ is homologous to B₁ and A₄ is homologous to B_4aand B_4b). In this example three alignments were sampled from this pairwise comparison. In step 2, all alignment candidates are sorted in descending order according to their score. Alignments that do not pass a user-defined threshold are discarded. The next step (3) enforces a 1:1 mapping of "matching" vertices. Genes are greedily assigned to one another based on the sorted alignments. The final step (4) merges the two chain graphs into a partial order graph (POG). Matching nodes are "fused" and non-matching nodes are retained as individual nodes.