Fig. 3
From: Aligning coding sequences with frameshift extension penalties
Illustration of the configurations of alignment considered in Lemma 1 for computing D(i, j) in cases 1 and 2. The right-most nucleotides of the sequences \(A[1\ldots i]\) and \(B[1\ldots j]\) A[1 .. i] and B[1 .. j] are represented using the character x. The nucleotides are colored according to the type of the codon to which they belong : IM codons in blue color, FSext codons in red color, InDel codons in green color and FSinit codons in black color. The nucleotides that appear in gray color are those belonging to codons whose type has not yet been decided. In such case, the table \(D_F\) is used in order to decide of the type of these codons subsequently and adjust the score accordingly