ArticleGenome biology and evolution2019
COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences.
Article in Genome biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed.
- Mitochondrial genome characterization and phylogenetic relationships of the subfamily Dipsadinae (Reptilia: Colubridae).Scientific reports · 2026Article
- Evolution and Functional Implications of Codon Usage Bias in Eukaryotes.Journal of molecular evolution · 2026Review
- Hurdles to horizontal gene transfer: species-specific effects of synonymous variation and plasmid copy number determine antibiotic resistance phenotype.Microbiology (Reading, England) · 2026Article
- RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU).BMC bioinformatics · 2025Article
- Translation of the downstream ORF from bicistronic mRNAs by human cells: Impact of codon usage and splicing in the upstream ORF.Protein science : a publication of the Protein Society · 2025Article
- Novel High-Quality Amoeba Genomes Reveal Widespread Codon Usage Mismatch Between Giant Viruses and Their Hosts.Genome biology and evolution · 2025Article
- Why HPV16? Why, now, HPV42? How the discovery of HPV42 in rare cancers provides an opportunity to challenge our understanding about the transition between health and disease for common members of the healthy microbiota.FEMS microbiology reviews · 2024Review
- GenRCA: a user-friendly rare codon analysis tool for comprehensive evaluation of codon usage preferences based on coding sequences in genomes.BMC bioinformatics · 2024Article
- Production of recombinant intact and N-terminal truncated lipoxygenase isozyme III expressed inFood chemistry. Molecular sciences · 2024Article
- Molecular insights into codon usage analysis of mitochondrial fission and fusion gene: relevance to neurodegenerative diseases.Annals of medicine and surgery (2012) · 2024Article
- Systematic analysis of the codon usage patterns of African swine fever virus genome coding sequences reveals its host adaptation phenotype.Microbial genomics · 2024Article
- Codon-optimization in gene therapy: promises, prospects and challenges.Frontiers in bioengineering and biotechnology · 2024Review
- Contribution of cryptochromes and photolyases for insect life under sunlight.Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology · 2023Article
- Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts.Pathogens (Basel, Switzerland) · 2023Article
- Article
- Application of codon usage and context analysis in genes up- or down-regulated in neurodegeneration and cancer to combat comorbidities.Frontiers in molecular neuroscience · 2023Article
- An investigation of codon usage pattern analysis in pancreatitis associated genes.BMC genomic data · 2022Article
- Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros.PLoS biology · 2022Article
- Composition and Codon Usage Pattern Results in Divergence of theJournal of fungi (Basel, Switzerland) · 2022Article
- Multiple Horizontal Acquisitions of Plant Genes in the Whitefly Bemisia tabaci.Genome biology and evolution · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Codon Usage Preferences (CUPrefs) describe the unequal usage of synonymous codons at the gene, chromosome, or genome levels. Numerous indices have been developed to evaluate CUPrefs, either in absolute terms or with respect to a reference. We introduce the normalized index COUSIN (for COdon Usage Similarity INdex), that compares the CUPrefs of a query against those of a reference and normalizes the output over a Null Hypothesis of random codon usage. The added value of COUSIN is to be easily interpreted, both quantitatively and qualitatively. An eponymous software written in Python3 is available for local or online use (http://cousin.ird.fr). This software allows for an easy and complete analysis of CUPrefs via COUSIN, includes seven other indices, and provides additional features such as statistical analyses, clustering, and CUPrefs optimization for gene expression. We illustrate the flexibility of COUSIN and highlight its advantages by analyzing the complete coding sequences of eight divergent genomes. Strikingly, COUSIN captures a bimodal distribution in the CUPrefs of human and chicken genes hitherto unreported with such precision. COUSIN opens new perspectives to uncover CUPrefs specificities in genomes in a practical, informative, and user-friendly way.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.