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The Needleman-Wunsch method for aligning DNA sequences
Chapter 2, Problem 12E(choose chapter or problem)
The Needleman-Wunsch method for aligning DNA sequences assigns 1 point whenever a mis-
match occurs, and 3 points whenever a gap (insertion or deletion) appears in a sequence. Assume that under certain conditions, the number of mismatches has mean 5 and standard deviation 2, and the number of gaps has mean 2 and standard deviation 1.
a. Find the mean of the Needleman-Wunsch score.
b. Assume the number of gaps is independent of the number of mismatches. Find the variance of the Needleman-Wunsch score.
Questions & Answers
QUESTION:
The Needleman-Wunsch method for aligning DNA sequences assigns 1 point whenever a mis-
match occurs, and 3 points whenever a gap (insertion or deletion) appears in a sequence. Assume that under certain conditions, the number of mismatches has mean 5 and standard deviation 2, and the number of gaps has mean 2 and standard deviation 1.
a. Find the mean of the Needleman-Wunsch score.
b. Assume the number of gaps is independent of the number of mismatches. Find the variance of the Needleman-Wunsch score.
ANSWER:
Answer :
Step 1 of 3 :
Given,
We have a method called Needleman - Wunsch method for aligning DNA sequences .
Which assigns 1 point whenever a mismatch occurs, and 3 points whenever a gap appears in a sequence.
We have to assume that the certain conditions, the number of mismatches has mean 5 and standard deviation 2. ( = 5 and = 5 )
The number of gaps has mean 2 and standard deviation 1.( = 2 and = 1 )
Let S denotes the Needleman-Wunsch score, then S = X + 3Y