Consider the problem of finding an optimum local multiplealignment of the three sequences
X = X1 X2 ……Xn1
Y = Y1 Y2 ……Yn2
Z = Z1 Z2 ……Zn3.
You are given a linear scoring schemes (α,β,γ) where α,β,γ∈{A,C,G,T,−}. In other words,the match scores and gap penalties arebuilt into a 5×5×5 array, and the contribution to the total scoreif α in sequence X aligns with β in sequence Y and γ in sequence Zis s(α,β,γ). You may further assume that s(α,β,γ) < 0 wheneverany of α, β or γ is a gap. Write out, in pseudo-code, the algorithmfor the generalisation of the SmithWaterman algorithm to
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