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密码子偏好性PR2（Parity Rule 2）绘图
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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、每个基因的A3，T3，C3，G3如何计算？是否有软件可以计算？ 2、４个同义密码子编码的氨基酸，有8个（alanine, arginine4 (CGA,CGT, CGG, CGC), glycine, leucine4 (CTA, CTT, CTG, CTC), proline,serine4 (TCA, TCT, TCG, TCC), threonine, and valine），是否把这8个氨基酸的A3，T3，C3，G3值分别进行平均，得到一个基因的A3，T3，C3，G3？ 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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