Models for alignment of an EST to genomic sequnce. The exhaustive model for aligning ESTs to genome DNA, showing portal states and span states is shown in Figure 4 (a). The portal states are match forward and match reverse, and these share a set of HSPs. The span states are intron forward and intron reverse, and may accommodate large gaps. These portal and span states are represented in the heuristic model shown in Figure 4 (b), with each transition represented by a different derived model, labelled A to E, corresponding to the SAR types show in Figure 2.