Figure 2.

Projection (middle) and refinement (bottom) of exons and transcripts from a closely related species (B) to a reference species (A) using genome-to-genome alignments (top). Following the initial projection (middle), exon endpoints may be adjusted to a better consensus splice site using a set of heuristics (bottom, left to right) that take into account the length of the unprojected end (trim), the distance to the next match (bound), the local profile of GenScan splice site scores, and existing same-species evidence.