RelativeCodonBiases

_namespace: SMRUCC.genomics.Analysis.SequenceTools.DNA_Comparative_

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

Methods

#ctor

1
SMRUCC.genomics.Analysis.SequenceTools.DNA_Comparative.RelativeCodonBiases.#ctor(SMRUCC.genomics.SequenceModel.FASTA.FastaToken)

ORF的核酸序列之中构建出密码子偏好属性

Parameter Name Remarks
Sequence ATG -> TGA这一段之间的ORF的核酸序列

__staticsOfMaxFrequencyCodon

1
SMRUCC.genomics.Analysis.SequenceTools.DNA_Comparative.RelativeCodonBiases.__staticsOfMaxFrequencyCodon(System.Char)

统计某一中氨基酸的编码偏好性

Parameter Name Remarks
AminoAcid -

Normalization

1
SMRUCC.genomics.Analysis.SequenceTools.DNA_Comparative.RelativeCodonBiases.Normalization(Microsoft.VisualBasic.ComponentModel.TripleKeyValuesPair{System.Double})

对Profile进行归一化处理

W

1
SMRUCC.genomics.Analysis.SequenceTools.DNA_Comparative.RelativeCodonBiases.W(SMRUCC.genomics.SequenceModel.NucleotideModels.Translation.Codon)

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 for the same amino acid a)

Parameter Name Remarks
Codon -