Author: Chan, Joseph M.; Rabadan, Raul
Title: Quantifying Pathogen Surveillance Using Temporal Genomic Data Document date: 2013_1_29
ID: u2t1x89m_38
Snippet: Shannon's entropy as a measurement of genetic diversity. Our measurement of pathogen surveillance incorporates the evolutionary rate, which contributes to population diversity. To measure genetic diversity directly, we chose to employ Shannon's entropy, a popular and intuitive measure that avoids cumbersome phylogenetic reconstruction, and applied it to the distribution of alleles at each nucleotide position within an alignment. This calculation .....
Document: Shannon's entropy as a measurement of genetic diversity. Our measurement of pathogen surveillance incorporates the evolutionary rate, which contributes to population diversity. To measure genetic diversity directly, we chose to employ Shannon's entropy, a popular and intuitive measure that avoids cumbersome phylogenetic reconstruction, and applied it to the distribution of alleles at each nucleotide position within an alignment. This calculation recovers the number of bits of information per base. Assuming the independence of each position, the total entropy of a population is the sum of the entropies of each base position of the alignment. To correct for bias stemming from a variable number of isolates (n), we estimate Shannon's entropy (H) for a given base position on the basis of the following algorithm of Miller et al., where m is the number of alleles (44):
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