GenomeSignatures

_namespace: SMRUCC.genomics.Analysis.SequenceTools.DNA_Comparative_

在本模块之中,所有的计算过程都是基于@”T:SMRUCC.genomics.SequenceModel.NucleotideModels.NucleicAcid”核酸对象的

Methods

__counts

1
SMRUCC.genomics.Analysis.SequenceTools.DNA_Comparative.GenomeSignatures.__counts(SMRUCC.genomics.SequenceModel.NucleotideModels.NucleicAcid,SMRUCC.genomics.SequenceModel.NucleotideModels.DNA[])

计算某些连续的碱基片段在序列之中的出现频率

Parameter Name Remarks
Sequence -
ns -

__counts_p

1
SMRUCC.genomics.Analysis.SequenceTools.DNA_Comparative.GenomeSignatures.__counts_p(SMRUCC.genomics.SequenceModel.NucleotideModels.NucleicAcid,SMRUCC.genomics.SequenceModel.NucleotideModels.DNA[])

计算某些连续的碱基片段在序列之中的出现频率(并行版本)

Parameter Name Remarks
Sequence -
ns -

CodonSignature

1
SMRUCC.genomics.Analysis.SequenceTools.DNA_Comparative.GenomeSignatures.CodonSignature(SMRUCC.genomics.SequenceModel.NucleotideModels.NucleicAcid,SMRUCC.genomics.SequenceModel.NucleotideModels.Translation.Codon)

CODON SIGNATURE

For a given collection of genes, let fX(1); fY(2); fZ(3) denote frequencies of the indicated nucleotide at codon sites 1, 2, and 3, respectively,
and let f(XYZ) indicate codon frequency. The embedded dinucleotide frequencies are denoted fXY(1, 2); fYZ(2, 3); and fXZ(1, 3). Dinucleotide
contrasts are assessed through the odds ratio pXY = f(XY)/f(X)f(Y).
In the context of codons, we define

1
2
3
pXY(1, 2) = fXY(1, 2)/fX(1)fY(2)
pYZ(2, 3) = fYZ(2, 3)/fY(2)fZ(3)
pXZ(1, 3) = fXZ(1, 3)/fX(1)fZ(3)

We refer to the profiles {pXY(1, 2)}; {pXZ(1, 3)}; {pYZ(2, 3)}, and also {pZW(3, 4)}, where 4(=1) is the first position of the next codon, as the
codon signature to be distinguished from the global genome signature

Parameter Name Remarks
Sequence -
Codon -

DinucleotideBIAS

1
SMRUCC.genomics.Analysis.SequenceTools.DNA_Comparative.GenomeSignatures.DinucleotideBIAS(SMRUCC.genomics.SequenceModel.NucleotideModels.NucleicAcid,SMRUCC.genomics.SequenceModel.NucleotideModels.DNA,SMRUCC.genomics.SequenceModel.NucleotideModels.DNA)

Dinucleotide relative abundance values (dinucleotide bias) are assessed through the odds ratio p(XY) = f(XY)/f(X)f(Y),
where fX denotes the frequency of the nucleotide X and fXY is the frequency of the dinucleotide XY in the
sequence under study.

DinucleotideBIAS_p

1
SMRUCC.genomics.Analysis.SequenceTools.DNA_Comparative.GenomeSignatures.DinucleotideBIAS_p(SMRUCC.genomics.SequenceModel.NucleotideModels.NucleicAcid,SMRUCC.genomics.SequenceModel.NucleotideModels.DNA,SMRUCC.genomics.SequenceModel.NucleotideModels.DNA)

Dinucleotide relative abundance values (dinucleotide bias) are assessed through the
odds ratio p(XY) = f(XY)/f(X)f(Y), where fX denotes the frequency of
the nucleotide X and fXY is the frequency of the dinucleotide XY in the
sequence under study.(并行版本)