GenomeSignatures

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.

计算某些连续的碱基片段在序列之中的出现频率

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)

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)

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

    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