The concept of Shannon's Entropy (Shannon, 1948) comes from the field of Information Theory. It measures the degree of uncertainty that exists in a system. In the case of multiple alignments, the Shannon entropy of each protein site can be computed according to:

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where Pi is the frequency of amino acid i in that site. If a column is completely conserved then Shannon entropy is 0. The maximum variability, where each amino acid occurs with frequency 1/20, yields an entropy of 4.32.

Shannon, C.E. (1948), "A Mathematical Theory of Communication", Bell Syst. Tech. J., 27, 379-423, 623-656




This document was last modified on February 6, 2006
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