ArticleCurrent genomics2012
Measures of compositional strand bias related to replication machinery and its applications.
Article in Current genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 20 citations in OpenAlex.
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- Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing.Journal of clinical medicine · 2019Article
- Reconsidering plasmid maintenance factors for computational plasmid design.Computational and structural biotechnology journal · 2019Review
- Optimization of amino acid replacement costs by mutational pressure in bacterial genomes.Scientific reports · 2017Article
- Energy efficiency trade-offs drive nucleotide usage in transcribed regions.Nature communications · 2016Article
- Codon Adaptation of Plastid Genes.PloS one · 2016Article
- Multiple Factors Drive Replicating Strand Composition Bias in Bacterial Genomes.International journal of molecular sciences · 2015Article
- Analysis of the Campylobacter jejuni genome by SMRT DNA sequencing identifies restriction-modification motifs.PloS one · 2015Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
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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 ∆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.
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