Author: Arlin Stoltzfus; Ryan W. Norris
Title: On the causes of evolutionary transition:transversion bias Document date: 2015_9_28
ID: 4xocqn6o_32
Snippet: One way to ask this question is to compare the ti:tv distinction to various biochemical distinctions. Any quantitative property of an amino acid can be used to create a conservative-vs-radical distinction, e.g., for a measure of the polarity of each amino acid, the "conservative" changes will be the ones with the least change in polarity. The AAindex database (Kawashima and Kanehisa 2000) has data on nearly 250 biochemical factors (see Methods). .....
Document: One way to ask this question is to compare the ti:tv distinction to various biochemical distinctions. Any quantitative property of an amino acid can be used to create a conservative-vs-radical distinction, e.g., for a measure of the polarity of each amino acid, the "conservative" changes will be the ones with the least change in polarity. The AAindex database (Kawashima and Kanehisa 2000) has data on nearly 250 biochemical factors (see Methods). The random sample of 25 factors from AAIndex shown in Figure 2 indicates that biochemical predictors typically are (1) considerably more powerful than the ti:tv distinction, and (2) considerably less powerful than EX and U (to view the full set of predictors, see Supplementary Material, section 3).
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