ArticleBMC bioinformatics2012
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Stepwise emergence of recombination suppression precedes fissiparous asexuality in the planarian Schmidtea mediterranea.Nature communications · 2026Article
- GenRCA: a user-friendly rare codon analysis tool for comprehensive evaluation of codon usage preferences based on coding sequences in genomes.BMC bioinformatics · 2024Article
- Article
- The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder.bioRxiv : the preprint server for biology · 2024Article
- Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species.Functional & integrative genomics · 2024Article
- Codon-optimization in gene therapy: promises, prospects and challenges.Frontiers in bioengineering and biotechnology · 2024Review
- Mitogenomic Phylogeny of Tonnoidea Suter, 1913 (1825) (Gastropoda: Caenogastropoda).Animals : an open access journal from MDPI · 2023Article
- Reading Frame Retrieval of Genes: A New Parameter of Codon Usage Based on the Circular Code Theory.Bulletin of mathematical biology · 2023Article
- Divergent paths in the evolutionary history of maternally transmitted clam symbionts.Proceedings. Biological sciences · 2022Article
- CompoDynamics: a comprehensive database for characterizing sequence composition dynamics.Nucleic acids research · 2022Article
- Codon usage bias.Molecular biology reports · 2022Review
- Article
- Genomewide comparative analysis of codon usage bias in three sequencedJournal of genetics · 2021Article
- Codon-based indices for modeling gene expression and transcript evolution.Computational and structural biotechnology journal · 2021Review
- COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences.Genome biology and evolution · 2019Article
- No signal of deleterious mutation accumulation in conserved gene sequences of extant asexual hexapods.Scientific reports · 2019Article
- Consequences of Asexuality in Natural Populations: Insights from Stick Insects.Molecular biology and evolution · 2018Article
- A novel framework for evaluating the performance of codon usage bias metrics.Journal of the Royal Society, Interface · 2018Article
- Effective purifying selection in ancient asexual oribatid mites.Nature communications · 2017Article
- Article
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundGenetic mutation, selective pressure for translational efficiency and accuracy, level of gene expression, and protein function through natural selection are all believed to lead to codon usage bias (CUB). Therefore, informative measurement of CUB is of fundamental importance to making inferences regarding gene function and genome evolution. However, extant measures of CUB have not fully accounted for the quantitative effect of background nucleotide composition and have not statistically evaluated the significance of CUB in sequence analysis.
resultsHere we propose a novel measure--Codon Deviation Coefficient (CDC)--that provides an informative measurement of CUB and its statistical significance without requiring any prior knowledge. Unlike previous measures, CDC estimates CUB by accounting for background nucleotide compositions tailored to codon positions and adopts the bootstrapping to assess the statistical significance of CUB for any given sequence. We evaluate CDC by examining its effectiveness on simulated sequences and empirical data and show that CDC outperforms extant measures by achieving a more informative estimation of CUB and its statistical significance.
conclusionsAs validated by both simulated and empirical data, CDC provides a highly informative quantification of CUB and its statistical significance, useful for determining comparative magnitudes and patterns of biased codon usage for genes or genomes with diverse sequence compositions.
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