Measures of Compositional Strand Bias Related to Replication Machinery and its Applications
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Summary
The measures of strand bias that have been proposed to date are reviewed, including the ∆GC 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.
- Type
- article
- Published
- 2012-03-01
- Cited by
- 19
- References
- 125
- Access
- Open access
- OpenAlex
- https://openalex.org/W1977147186
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:18308478
Keywords
Predictability, Skew, Biology, Computational biology, Genetics
References
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- GC-compositional strand bias around transcription start sites in plants and fungi
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- G-language System as a platform for large-scale analysis of high-throughput omics data
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- Wavelet-based method to disentangle transcription- and replication-associated strand asymmetries in mammalian genomes
- G-language genome analysis environment with REST and SOAP web service interfaces
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- The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics
- In Silico Prediction of the Origin of Replication among Bacteria: A Case Study of Bacteroides thetaiotaomicron
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Cited by
- Variation and constraints in species-specific promoter sequences.
- Analysis of the Campylobacter jejuni Genome by SMRT DNA Sequencing Identifies Restriction-Modification Motifs
- Multiple Factors Drive Replicating Strand Composition Bias in Bacterial Genomes
- Energy efficiency trade-offs drive nucleotide usage in transcribed regions
- Codon Adaptation of Plastid Genes
- Optimization of amino acid replacement costs by mutational pressure in bacterial genomes
- Beyond the Linear Genome: Comprehensive Determination of the Endogenous Circular Elements in C. elegans and Human Genomes via an Unbiased Genomic-Biophysical Method
- Methods for analyzing next-generation sequencing data IX.Genome annotation, visualization, and registration to DDBJ
- Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of the Arabidopsis originome
- Reconsidering plasmid maintenance factors for computational plasmid design
- Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing
- Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
- Cyanobacterial multi-copy chromosomes and their replication
- Shewanella algae and Morganella morganii Coinfection in Cobra-Bite Wounds: A Genomic Analysis
- Molecular analysis of the replication functions of the bifidobacterial conjugative megaplasmid pMP7017
- The topography of DNA replication origins in Eukarya: GGN clusters, landmark nucleosomes, CDC6 and G4 structures
- Genome size and nucleotide skews as predictors of bacterial growth rate
- Plasmids and Their Hosts
- Genome size and nucleotide skews as predictors of bacterial growth rate
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