Site analysis. Selective pressures and Likelihood-ratio-tests in protamine 1 and protamine 2 sequences.

Parameter estimation and likelihood scores under models of variable ω ratios among sites for protamine 1, cleaved region of protamine 2 and the mature form of protamine 2. The data have N sequences, each of Lc codons after alignment gaps are removed. Differences between log-likelihood values of models with 99% statistical significance level for 2 d. f. are indicated in ** and with 95% of statistical significance in *. The proportion of sites under positive selection (p1), or under selective constraint (p0) and parameters p and q for the beta distribution are given. Positively selected sites (PSS) with a posterior probability >0.95 (*) and >0.99 (**) in a Bayes Empirical Bayes are indicated. Selectives pressures are shown as proportion of amino acid sites for different classes of selective regimes. Class 1: sites under purifying selection (01). Proportions of sites in each selective class were also calculated for DNA-anchoring domains, phosphorylation motifs and cleaving sites.

本数据集针对鱼精蛋白1（protamine 1）、鱼精蛋白2（protamine 2）的切割区域以及鱼精蛋白2的成熟形式，完成了位点间可变ω比值模型下的参数估计与似然得分计算。数据集包含N条序列，移除比对空位（alignment gaps）后，每条序列剩余Lc个密码子。以自由度为2（2 d. f.）的统计检验为例，不同模型的对数似然值差异在99%统计显著性水平下以**标注，95%统计显著性水平下以*标注。本数据集同时给出了正选择位点占比（p1）、纯化选择位点占比（p0），以及β分布的参数p与q。贝叶斯经验贝叶斯（Bayes Empirical Bayes）分析中，后验概率大于0.95的正选择位点（PSS，Positively Selected Sites）以*标注，大于0.99的正选择位点以**标注。选择压力以不同选择模式下的氨基酸位点占比进行呈现，其中类别1代表处于纯化选择的位点（01）。此外，还针对DNA锚定结构域（DNA-anchoring domains）、磷酸化基序（phosphorylation motifs）以及切割位点（cleaving sites），分别计算了各选择类别下的位点占比。