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CHAPTER 5 PROBLEMS


	Introduction
	Problem 1
	Problem 2
	Problem 3
	Problem 4
	Problem 5
	Problem 6
	Problem 7
	Problem 8
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8. This problem explores the information content of a scoring matrix by the relative entropy method (ignores background frequencies). Read the notes on information content of sequences on page 213 before trying this problem.

Calculate the entropy or uncertainty (H_c) for each column and for the entire matrix.
Calculate the decrease in uncertainty or amount of information (R_c) for column 1 due to these data (for DNA, R_c = 2 – H_c and for proteins, R_c = 4.32 – H_c).
Calculate the amount that the uncertainty is reduced (or the amount of information contributed) for each base in column 1.

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