(3) Protein scoring matrices, such as the BLOSUM family, are often characterized by their relative entropy lij Σ 9ij ij where qj is the implied joint probability distribution of letters i and j, and pi is the probability distribution of a single letter i. (a) What properties of the relative entropy make it useful for comparing scor- ing matrices? (b) What would be more appropriate for comparing extremely divergent pro- tein sequences, a scoring matrix with large relative entropy or small relative entropy?

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(3) Protein scoring matrices, such as the BLOSUM family, are often characterized
by their relative entropy
Ei og )
lij
Σ
9ij
ij
where qj is the implied joint probability distribution of letters i and j, and pi
is the probability distribution of a single letter i.
(a) What properties of the relative entropy make it useful for comparing scor-
ing matrices?
(b) What would be more appropriate for comparing extremely divergent pro-
tein sequences, a scoring matrix with large relative entropy or small relative
entropy?
Transcribed Image Text:(3) Protein scoring matrices, such as the BLOSUM family, are often characterized by their relative entropy Ei og ) lij Σ 9ij ij where qj is the implied joint probability distribution of letters i and j, and pi is the probability distribution of a single letter i. (a) What properties of the relative entropy make it useful for comparing scor- ing matrices? (b) What would be more appropriate for comparing extremely divergent pro- tein sequences, a scoring matrix with large relative entropy or small relative entropy?
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