An Improved Implementation of Codon Adaptation Index
Open accessAbstract
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.
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The codon optimization applied to BNT-162b2 and mRNA-1273 leads to a much increased CAI and ITE for the two vaccine mRNAs.
“The codon optimization applied to BNT-162b2 and mRNA-1273 leads to a much increased codon adaptation index (CAI) [21,22] and index of translation efficiency (ITE) [11,36] for the two vaccine mRNAs.”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [22]
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Sharp, P. M., & Li, W.-H. (1987) · Nucleic Acids Research · doi:10.1093/nar/15.3.1281 · Cited by 3,992 · see citing works
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Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines
Xia, X. (2021) · Vaccines · doi:10.3390/vaccines9070734 · Cited by 201 · see citing works
Self-citationFactors effecting expression of vaccines in microalgae
Surzycki, R., Greenham, K., Kitayama, K., Dibal, F., Wagner, R., Rochaix, J.-D., Ajam, T., & Surzycki, S. (2009) · Biologicals · doi:10.1016/j.biologicals.2009.02.005 · Cited by 185 · see citing works
- Authors
- Xia, X.
- Affiliations
- University of Ottawa (CA)
- Corresponding author
- Xia, Xuhua
- ORCID
- Xia, Xuhua
- Venue
- Evolutionary Bioinformatics
- Publisher
- SAGE Publications
- Published
- 2007-01
- Volume
- 3
- Pages
- 53-8
- ISSN
- 1176-9343 (ISSN-L)
- PMC
- PMC2684136
- OpenAlex
- W4232709127
- Cited by
- 109
- References
- 1
- Citations by year
- 2026: 6 · 2025: 3 · 2024: 9 · 2023: 9 · 2022: 7 · 2021: 5 · 2020: 5 · 2019: 3 · 2018: 9 · 2017: 5 · 2016: 3 · 2015: 4 · 2014: 9 · 2013: 5 · 2012: 10
- FWCI
- 1.11
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Evolutionary Bioinformatics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- PubMed
- Funders
- Natural Sciences and Engineering Research Council of Canada
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- codon adaptation index, gene expression, translation efficiency, systematic bias, computational implementation, codon usage
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