密码子偏好性PR2(Parity Rule 2)绘图

PR2(Parity Rule 2)绘图分析如何做?PR2(Parity Rule 2),有的人也叫奇偶偏好分析。
我选取一个病毒的46个不同毒株的编码区序列,即有46个核苷酸序列。
现在要用这46个序列对这个病毒进行PR2(Parity Rule 2)绘图。
根据文献,需要计算A3,T3,C3,G3的含量(fraction),再算A/(A + T)]和G/(G + C)。而且文献里面提到要用下列氨基酸的这些密码子的A3,T3,C3,G3值更有说服力:four-codon amino acids:alanine, arginine4 (CGA,CGT, CGG, CGC), glycine, leucine4 (CTA, CTT, CTG, CTC), proline,serine4 (TCA, TCT, TCG, TCC), threonine, and valine.

存在的问题:
1、对每个病毒株:8个氨基酸,每个氨基酸四个密码子,即有32个密码子,而且这32个密码子是不一样的。我个人理解,每个氨基酸应该有一组A3,T3,C3,G3值,那么是否需要合并8组氨基酸A3,T3,C3,G3的值得到一组A3,T3,C3,G3?
2、A3,T3,C3,G3究竟如何计算?
3、46个病毒毒株,是不是意味着PR2(Parity Rule 2)图中有46个点?


原始的参考文献里面是这么介绍PR2(Parity Rule 2):
标题:Near Homogeneity of PR2-Bias Fingerprints in the Human Genome and
Their Implications in Phylogenetic Analyses
PR2-bias Plot的介绍. Plotting AT-bias [A/(A + T)] as the ordinate and
GC-bias [G/(G + C)] as the abscissa shows PR2-biases as a unique
pattern (Sueoka 1995). The center of the plot, where both coordinates
are 0.5, is the place where A=T and G=C (PR2). A vector from the
center represents the extent and direction of biases from PR2. PR2 bias
plots are particularly informative when PR2 biases at the third codon
position of the four-codon amino acids of individual genes are plotted.
In this case, “A3/(A3 + T3) | 4” and “G3/(G3 + C3) | 4” are plotted as theordinate and abscissa, respectively. Here “| 4” denotes the four-codon
amino acids. The four-codon amino acids are alanine, arginine4 (CGA,
CGT, CGG, CGC), glycine, leucine4 (CTA, CTT, CTG, CTC), proline,
serine4 (TCA, TCT, TCG, TCC), threonine, and valine.
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