Abstract
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 ΔGC skew, the B1 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.
Keywords: Nucleotide composition bias, bacterial replication, GC skew, replication-related mutations, compositional asymmetry, DNA, eukaryotes, prokaryotes, Gene Orientation, Predictability Score
Current Genomics
Title: Measures of Compositional Strand Bias Related to Replication Machinery and its Applications
Volume: 13 Issue: 1
Author(s): Kazuharu Arakawa and Masaru Tomita
Affiliation:
Keywords: Nucleotide composition bias, bacterial replication, GC skew, replication-related mutations, compositional asymmetry, DNA, eukaryotes, prokaryotes, Gene Orientation, Predictability Score
Abstract: 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 ΔGC skew, the B1 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.
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Cite this article as:
Arakawa Kazuharu and Tomita Masaru, Measures of Compositional Strand Bias Related to Replication Machinery and its Applications, Current Genomics 2012; 13 (1) . https://dx.doi.org/10.2174/138920212799034749
DOI https://dx.doi.org/10.2174/138920212799034749 |
Print ISSN 1389-2029 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5488 |
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