Fig. 4.

Stepping stone algorithm–the three diagonal lines represent the three HSPs. The stars represent alignment pins. The lighter grey areas represent the search subspaces that are actually used in the heuristic method. The optimal algorithm uses the entire rectangle in dark grey. The block diagram shows the optimal spliced alignment where grey boxes represent an exon and the thin lines represent an intron. This figure was reproduced from Arumugam et al. (2006).