Answer Happy

4. Questions 4-5 will test your understanding of the optimality of global pairwise sequence alignment (that is, what the score of an alignment is and what makes an alignment optimal). Consider the scoring matrix M for alphabet Σ = {A, C, T, G} with the following entries: Mo,o = 5 for every σ € Σ. Mo,d' = 2 for every o, o' € Σ and o ‡ o'. Mor = -2 for every σ € Σ. Mo = -4 for every σ € Σ. What is the score of the following alignment: X'=AC--CT Y'=TACGGT Enter your answer below as a single number. ANS 5. Let X = AC and Y = GG be two DNA sequences (= {A, C, T, G}), and consider the scoring matrix M given by: Maa = 6 for every σ € Σ. Mo,a¹ = 2 for every σ, o' € Σ and o # o'. M₁ = M_₁= -4 for every σ € >. Under this scoring matrix, which pair of sequences below is the optimal global alignment of X and Y? O X'= AC and Y' = GG. O X'= AC- and Y' - GG. O X'= -AC- and Y' = -GG-. O X'= AC- and Y' = -GG. O X'=A-C- and Y' = -G- G.

6. Let B (m, n) denote the number of global alignments of two sequences X and Y of lengths m and n, respectively. A recursive formula for B (m, n) is: O B(m, n) = nB(m, n − 1). O B(m, n) = m B (m – 1,n). OB(m, n) = m B (m-1, n) +n· B(m, n − 1). B(m, n) = B(m 1, n) + B(m, n − 1). O B(m, n) = B(m – 1, n) + B(m – 1, n − 1) + B(m, n − 1).