Table 2 The correspondence between DB(G A , G B , k) and BP(G A , G B , k) (under the single-stranded representation).
From: What is the difference between the breakpoint graph and the de Bruijn graph?
| Â | DB(GA, GB, k) | BP(GA, GB, k) |
|---|---|---|
(k-1)-mer | vertex | black directed edge (E1) |
k-mer | directed edge | directed edge (E2) |
color | red/blue/green directed edge blue in G A , red in G B , green in both G A and G B | red/blue/green directed edge (E2) blue in G A , red in G B , green in both G A and G B |
glue | vertex | E 1 |
synteny block as a path | vertex-green edge-. . .-vertex | E1 -green E2-. . .-E1 |
breakpoint region as a path | red edge-vertex. . .-red edge blue edge-vertex-. . .-blue edge | red E2 -E1-. . .-red E2 blue E2 -E1-. . .-blue E2 |
condensing paths into edges | red edge-vertex-red edge → red edge blue edge-vertex-blue edge → blue edge green edge-vertex-green edge → green edge | red E2 -E1-red E2 → red E2 blue E2-E1-blue E2 → blue E2 green E2-E1-green E2 → green E2 |
after condensation | CDB(G A , G B , k) | CBP(G A , G B , k) |
synteny block in condensed graph | vertex-green edge-vertex | E1-green E2-E1 |
breakpoint region in condensed graph | red edge blue edge | red E2 blue E2 |