ArticleEvolutionary bioinformatics online2007
An improved implementation of codon adaptation index.
Article in Evolutionary bioinformatics online, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 79 citations in OpenAlex.
- Stoichiometry-induced differential selection on codon optimization among ribosomal protein genes in bacterial species.Molecular biology and evolution · 2026Article
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- mRNA therapeutics: Transforming medicine through innovation in design, delivery, and disease treatment.Molecular therapy. Nucleic acids · 2025Review
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- Decoding codon usage in human papillomavirus type 59.Virus genes · 2025Article
- Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51.Polish journal of microbiology · 2024Article
- Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species.Microorganisms · 2024Article
- Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages.Virus evolution · 2024Article
- A small stretch of poor codon usage at the beginning of dengue virus open reading frame may act as a translational checkpoint.BMC research notes · 2023Article
- Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage.PLoS genetics · 2022Article
- Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases.Computational and structural biotechnology journal · 2022Review
- Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.Frontiers in cellular and infection microbiology · 2022Article
- Coupled protein synthesis and ribosome-guided piRNA processing on mRNAs.Nature communications · 2021Article
- Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines.Vaccines · 2021Article
- A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses.Gene reports · 2021Article
- ΦX174 Attenuation by Whole-Genome Codon Deoptimization.Genome biology and evolution · 2021Article
- Genome-Wide Analysis of Chemosensory Protein Genes (CSPs) Family in Fig Wasps (Hymenoptera, Chalcidoidea).Genes · 2020Article
- Analysis of Nipah Virus Codon Usage and Adaptation to Hosts.Frontiers in microbiology · 2019Article
- DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution.The Journal of heredity · 2017Article
- How Changes in Anti-SD Sequences Would Affect SD Sequences inG3 (Bethesda, Md.) · 2017Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Codon adaptation index is a widely used index for characterizing gene expression in general and translation efficiency in particular. Current computational implementations have a number of problems leading to various systematic biases. I illustrate these problems and provide a better computer implementation to solve these problems. The improved CAI can predict protein production better than CAI from other commonly used implementations.
Indexed as
Identifiers
19461982PMC2684136W2152777703What 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.