ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2008
Comparison of correspondence analysis methods for synonymous codon usage in bacteria.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Codon usage bias and molecular evolution ofFrontiers in genetics · 2026Article
- Giant extrachromosomal element "Inocle" potentially expands the adaptive capacity of the human oral microbiome.Nature communications · 2025Article
- Characteristics and phylogenetic distribution of megaplasmids and prediction of a putative chromid inComputational and structural biotechnology journal · 2024Article
- Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species.Functional & integrative genomics · 2024Article
- Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy.Cells · 2022Article
- Whole genome sequencing and comparative genomic analyses of Pseudomonas aeruginosa strain isolated from arable soil reveal novel insights into heavy metal resistance and codon biology.Current genetics · 2022Article
- Tempo of Degeneration Across Independently Evolved Nonrecombining Regions.Molecular biology and evolution · 2022Article
- An ancient retroviral RNA element hidden in mammalian genomes and its involvement in co-opted retroviral gene regulation.Retrovirology · 2021Article
- Characterization of the First Cultured Psychrotolerant Representative ofMicrobiology spectrum · 2021Article
- A Crosstalk on Codon Usage in Genes Associated with Leukemia.Biochemical genetics · 2021Article
- 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
- Codon Usage in theViruses · 2019Article
- Variation and selection on codon usage bias across an entire subphylum.PLoS genetics · 2019Article
- Revisiting the Taxonomy of the GenusFrontiers in microbiology · 2018Article
- Gene expression, nucleotide composition and codon usage bias of genes associated with human Y chromosome.Genetica · 2017Article
- Codon usage in Alphabaculovirus and Betabaculovirus hosted by the same insect species is weak, selection dominated and exhibits no more similar patterns than expected.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2016Article
- Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae.International journal of molecular sciences · 2016Article
- Codon Adaptation of Plastid Genes.PloS one · 2016Article
- Genome Data Exploration Using Correspondence Analysis.Bioinformatics and biology insights · 2016Review
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4 authors.
Funding
Abstract
Synonymous codon usage varies both between organisms and among genes within a genome, and arises due to differences in G + C content, replication strand skew, or gene expression levels. Correspondence analysis (CA) is widely used to identify major sources of variation in synonymous codon usage among genes and provides a way to identify horizontally transferred or highly expressed genes. Four methods of CA have been developed based on three kinds of input data: absolute codon frequency, relative codon frequency, and relative synonymous codon usage (RSCU) as well as within-group CA (WCA). Although different CA methods have been used in the past, no comprehensive comparative study has been performed to evaluate their effectiveness. Here, the four CA methods were evaluated by applying them to 241 bacterial genome sequences. The results indicate that WCA is more effective than the other three methods in generating axes that reflect variations in synonymous codon usage. Furthermore, WCA reveals sources that were previously unnoticed in some genomes; e.g. synonymous codon usage related to replication strand skew was detected in Rickettsia prowazekii. Though CA based on RSCU is widely used, our evaluation indicates that this method does not perform as well as WCA.
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