Fig. 9

Dynamic score-based banding applied on a graph. Top: an alignment graph. Bottom: The DP matrix for aligning a read to the above graph. The arrows show the correspondence between nodes in the graph and columns in the DP matrix. The dotted lines separate the nodes. The gray area represents parts of the DP matrix which are calculated, and the parts in the white area are not calculated. At each fork, the band spreads to all out-neighbors. The score-based banding implicitly limits the exploration of the alternate paths; as the scores in the alternate paths become worse than the optimal path, the explored part shrinks until finally the exploration stops completely. The blue line shows the backtrace path