Figure 8.

The construction of one connected component in the repeat domain graph of C. elegans. (a) In the initial A-Bruijn graph, seq. H (Ce000444) and seq. F (Ce000067) are in a same connected component, but many short cycles fragment repeat domains in this graph. (b) However, in the graph after the standard bulge and whirl removal procedures (for example, from ABA), due to a whirl removal process starting from the green edge in (a), all glues between seq. H and seq. F are lost and seq. H is in a separate connected component. (c) The repeat domain graph constructed with the new whirl handling algorithm and the bulge removal procedure; now seq. H and seq. F are shown to share some significant edges.