Figure 3
From: Integrating alternative splicing detection into gene prediction
Detail of EuGène's directed acyclic graph and algorithm. The zoomed region contains the two first nucleotides of the example sequence of Figure 3 (C at position i - 1, and A at position i), and two annotation tracks (UTR5' for j and exon in frame 2 for j + 1). The contents edges c connect the l vertices to the following r vertices of the same track. Transition edges t are either horizontal and link the r vertices to the l vertices of the same track, or transversal and link the r vertices to all possible l vertices according to the occurrence of a biological signal in the sequence. In this example, between 
and 
a vertex 
allows the transition from the UTR5' track at position i - 1 to the exonic track at i because the A nucleotide at position i is the first nucleotide of a potential start codon ATG. The dynamic programming algorithm used in EuGÈNE determines, for each vertex r, which vertex precedes r in the optimal path. In this example, at position i for the track j the best path leading to 
from the left has a weight 
(only one origin is possible). For the track j + 1, the best path leading to 
will be attributed a weight of either 
, whatever the lower.