FIG. 2.

The canonical antibody graph for different values of (arcs corresponding to the V, D, and J gene segments are colored blue, green, and red, respectively) constructed for all alleles (left) and all consensus gene-segments (right). All nonbranching paths are collapsed to a single arc, and at each junction, a dummy node is created to connect V gene segments to D gene segments, and D gene segments to J gene segments; these arcs are colored black. These graphs are constructed with (a and d), (b and e), and (c and f). Panel (b) shows V, D, and J gene segments completely separated, while (a) shows considerably more sharing of arcs in the V segments, and some shared in the D gene segments. Increasing the value of (c) greatly simplifies the relationship among V gene segments. This is not a feasible parameter for our purposes (as no D segments are captured) but does show the complexity of V gene segments. In the case of , the graph becomes disconnected (and green edges disappear), since it exceeds the length of the longest D gene segment.