Figure 1

SNAP HMM state diagram Each state of the HMM is represented by a shape and transitions between the states are represented by arrows. States include N: intergenic, Es: single-exon gene, Ei: initial exon, Et terminal exon, E0–E2: exons in phase 0–2, I0–I2: introns in phases 0–2 (subscript of T, TA, or TG denotes the last bp or two bp of the intron – this is used to prevent in-frame stop codons across splice junctions).