Answer to Question #154928 in Bioinformatics for vaibhav

Question #154928

There are two hypothetical “one column” multiple sequence alignments. In the first alignment of N sequences, every residue is a tyrosine. In the second alignment, there are N-1 tyrosines and one proline.

(b) Given that the BLOSUM62 Y ↔ Y score is 7, calculate the score of the first alignment as a function of N. This is SY N (N).

(c) Given that the BLOSUM62 Y ↔ P score is -4, calculate the score of the second alignment as a function of N. This is SY N-1 P1 (N).(d) Evaluate and simplify the following expression, representing the fractional difference between the two different sequence alignments.

f (N) = [SY N (N) - SY N-1 P1 (N)]/ SY N (N)

(e) Construct a plot of the expression you derived in part (c), and explain why this scoring behavior is incorrect

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