Figure 2

EuGène's directed acyclic graph for a short example sequence. For simplicity purposes, only the forward strand is considered. The DNA sequence is shown above the graph. Horizontal tracks represent the different possible annotations: intergenic (bottom), UTR 5' and 3', exon in the 3 frames, intron in 3 phases (the phase of an intron is defined according to the splicing position in the last codon of the previous exon). On each track, 2 vertices are used to represent each nucleotide. These 2 vertices are linked horizontally by a contents and a transition edge (see the text and Figure 4 for details). Dotted arrows show occurrences of biological signals (like start/stop codons and donor/acceptor splice sites). They produce additional transition edges at the corresponding position. Since this version of EuGÈNE does not include any promoter or polyA site prediction tool, transitions from intergenic to UTR and vice-versa are allowed at every nucleotide position. All consistent gene structures can be represented by a path connecting the initial and terminal vertices and .