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Measures of Relative Codon Biases
CAI: codon adaptation index
This specifies a reference set of genes, almost invariably, H, chosen from among “highly expressed genes.”
Defining W(xyz) = f(xyz)/max(xyz[a])*f(xyz,H) as the ratio of the frequency of the codon (xyz) to the maximal codon frequency in H for the same amino acid a ,the CAI of a gene of length L is taken as PI(Wi)^(1/L) (the log average), where i refers to the ith codon of the gene and w is calculated as above.
H 集合是所选择的高表达量的参考基因
01 Syntax
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| .ctor | 1 | ORF的核酸序列之中构建出密码子偏好属性 |
| W | 1 | 计算 W(Codon) 即计算当前的密码子与编码相同氨基酸的最高频率的密码子的商 (Defining W(xyz) = f(xyz)/max(xyz[a])*f(xyz,H) as the ratio of the frequency of the codon (xyz) to the maximal codon frequency in H f… |
| staticsOfMaxFrequencyCodon | 1 | 统计某一中氨基酸的编码偏好性 |
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| CodonFrequencyStatics | 1 | CodonFrequency.AminoAcid就是这个字典的键名key |
04 Members
FastaSeq, GeneticCodes)ORF的核酸序列之中构建出密码子偏好属性
| Name | Type | Description |
|---|---|---|
nt | FastaSeq | ATG -> TGA这一段之间的ORF的核酸序列 |
Codon)即计算当前的密码子与编码相同氨基酸的最高频率的密码子的商 (Defining W(xyz) = f(xyz)/max(xyz[a])*f(xyz,H) as the ratio of the frequency of the codon (xyz) to the maximal codon frequency in H for the same amino acid a)
| Name | Type | Description |
|---|---|---|
Codon | Codon | - |
Char, GeneticCodes)统计某一中氨基酸的编码偏好性
| Name | Type | Description |
|---|---|---|
aminoAcid | Char | 可能会有集中密码来编码相同的一个氨基酸 |
CodonFrequency.AminoAcid就是这个字典的键名key