Figure 2.

Location of a new EST internal factor s_i+1 given previous computed factors s₂, ..., s_i. (a) Consecutive sequence components c₁ ... c_j are tested to find the first one that allows the identification of a genomic region that optimally aligns factor s_i+1 (i.e. alignment extension on one or both sides of the component): such a region is determined in (b) by the component c_j. Figure (b) shows that some intervening positions (sequence x) may occur between factor s_i and s_i+1. Indeed, in this case the placement of s_i+1 gives the correct right end of previous factor s_i, since the larger factor inducing canonical splice sites on the genomic sequence can be optimally aligned before s_i+1 thus leading to an optimal location of both s_i and s_i+1.