Figure 9

Genome alignment cycles have a one-to-one correspondence only in the structure of Enredo graphs. (A) A cycle in the Enredo graph structure may correspond to several overlapping cycles in the alignment graph structure. In this example, two cycles in the alignment graph structure are shaded in red and blue. (B) Cycles caused by inversions appear only in the Enredo graph structure. In this example, the upper cycle in the Enredo graph structure is due to an inversion in block A, hence, does not appear in the A-Bruijn graph structure.