Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.
Curr Genomics. 2012 Mar;13(1):4-15. doi: 10.2174/138920212799034749.
The compositional asymmetry of complementary bases in nucleotide sequences implies the existence of a mutational or selectional bias in the two strands of the DNA duplex, which is commonly shaped by strand-specific mechanisms in transcription or replication. Such strand bias in genomes, frequently visualized by GC skew graphs, is used for the computational prediction of transcription start sites and replication origins, as well as for comparative evolutionary genomics studies. The use of measures of compositional strand bias in order to quantify the degree of strand asymmetry is crucial, as it is the basis for determining the applicability of compositional analysis and comparing the strength of the mutational bias in different biological machineries in various species. Here, we review the measures of strand bias that have been proposed to date, including the ∆GC skew, the B(1) index, the predictability score of linear discriminant analysis for gene orientation, the signal-to-noise ratio of the oligonucleotide bias, and the GC skew index. These measures have been predominantly designed for and applied to the analysis of replication-related mutational processes in prokaryotes, but we also give research examples in eukaryotes.
核苷酸序列中互补碱基的组成不对称性意味着 DNA 双链中存在突变或选择偏向，这种偏向通常由转录或复制中的链特异性机制形成。这种基因组中的链偏向，通常通过 GC 倾斜图可视化，用于计算预测转录起始位点和复制原点，以及进行比较进化基因组学研究。使用组成链偏向的度量来量化链不对称的程度至关重要，因为它是确定组成分析适用性和比较不同生物机制在不同物种中的突变偏向强度的基础。在这里，我们回顾了迄今为止提出的链偏向度量，包括 ∆GC 倾斜、B(1) 指数、线性判别分析的基因取向预测分数、寡核苷酸偏向的信噪比和 GC 倾斜指数。这些度量主要用于分析原核生物中与复制相关的突变过程，但我们也给出了真核生物的研究示例。
