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Activity Number: 188
Type: Topic Contributed
Date/Time: Monday, July 30, 2007 : 2:00 PM to 3:50 PM
Sponsor: IMS
Abstract - #309691
Title: Measures of Volatility and Valency for Serially Sampled Nucleotide Sequences
Author(s): John O'Brien*+
Companies: University of California, Los Angeles
Address: Box 951766 - Biomathematics, Los Angeles, CA, 90095-1766,
Keywords: sequence volatility ; serially sampled ; Markov process ; phylogenetics
Abstract:

(Plotkin and Dushoff, 2004) showed that it is possible to define a sequence volatility measure, giving the number of amino acid changes accessible within one nucleotide substitution of a given codon. We define a related quantity, the valency of codon, which is the volatility modulo the number of different residues available. Starting with the Goldman/Yang matrix for codon changes, we partition the process via a Markov counting process (Minin, 2007) and are able to derive pairwise distances for both valency and volatility. In the case of influenza A hemagglutinin, we show that after zoonotic transfer the valency of the sequence increases substantially over time, with the most dramatic alterations at known active sites in the protein. We conclude by showing that these changes are independent of shifts in the underlying nucleotide distribution.

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Revised September, 2007