ArticleNucleic acids research2002
Use and misuse of correspondence analysis in codon usage studies.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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73 citing papers in PubMed.
- Reassessing Murinae phylogeny: integrated mitogenomic and codon usage evidence challenges the sister relationship of Micromyini and Vernayini.BMC genomics · 2026Article
- Integrative chloroplast omics in citrus: computational insights into genomic structural adaptation and phylogenetic relationships from 35 species.Frontiers in plant science · 2026Article
- NSUN2-tRNACellular & molecular biology letters · 2025Article
- Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.Frontiers in plant science · 2025Article
- Comparative Analysis of the Codon Usage Pattern in the Chloroplast Genomes of Gnetales Species.International journal of molecular sciences · 2024Article
- Mitochondrial genomes of Macropsini (Hemiptera: Cicadellidae: Eurymelinae): Structural features, codon usage patterns, and phylogenetic implications.Ecology and evolution · 2024Article
- Structural Characteristics and Phylogenetic Analysis of the Mitochondrial Genomes of FourGenes · 2023Article
- Mutational Bias and Natural Selection Driving the Synonymous Codon Usage of Single-Exon Genes in Rice (Oryza sativa L.).Rice (New York, N.Y.) · 2023Article
- Correspondence analysis for dimension reduction, batch integration, and visualization of single-cell RNA-seq data.Scientific reports · 2023Article
- Adaptive evidence of mitochondrial genes in Pteromalidae and Eulophidae (Hymenoptera: Chalcidoidea).PloS one · 2023Article
- Article
- The pattern of coding sequences in the chloroplast genome of Atropa belladonna and a comparative analysis with other related genomes in the nightshade family.Genomics & informatics · 2022Article
- Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage.PLoS genetics · 2022Article
- Codon usage bias.Molecular biology reports · 2022Review
- Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus.Pathogens (Basel, Switzerland) · 2021Article
- Analysis of Codon Usage of Speech GeneBiology · 2021Article
- The insertion of a mitochondrial selfish element into the nuclear genome and its consequences.Ecology and evolution · 2020Article
- Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design.Journal of virological methods · 2020Article
- Multivariate analyses of codon usage of SARS-CoV-2 and other betacoronaviruses.Virus evolution · 2020Article
- Comparative evolutionary genomics of Corynebacterium with special reference to codon and amino acid usage diversities.Genetica · 2018Article
13 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Correspondence analysis has frequently been used for codon usage studies but this method is often misused. Because amino acid composition exerts constraints on codon usage, it is common to use tables containing relative codon frequencies (or ratios of frequencies) instead of simple codon counts to get rid of these amino acid biases. The problem is that some important properties of correspondence analysis, such as rows weighting, are lost in the process. Moreover, the use of relative measures sometimes introduces other biases and often diminishes the quantity of information to analyse, occasionally resulting in interpretation errors. For instance, in the case of an organism such as Borrelia burgdorferi, the use of relative measures led to the conclusion that there was no translational selection, while analyses based on codon counts show that there is a possibility of a selective effect at that level. In this paper, we expose these problems and we propose alternative strategies to correspondence analysis for studying codon usage biases when amino acid composition effects must be removed.
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