Generating the search subspace given three high-scoring segment pairs (HSPs) in the Stepping Stone algorithm. The three diagonal lines represent the three HSPs. The stars represent alignment pins. The lighter blue areas represent the search subspaces that are actually used in the heuristic method. The optimal algorithm uses the entire rectangle in blue. The block diagram shows the optimal spliced alignment where blue boxes represent an exon and the thin lines represent an intron.
Arumugam et al. Genome Biology 2006 7(Suppl 1):S5 doi:10.1186/gb-2006-7-s1-s5