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The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications

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Sharp, Paul M., Li, Wen-Hsiung·1987·Nucleic Acids Research

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Abstract

A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed. The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression.

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Authors: Sharp, P. M., & Li, W.-H.
Affiliations: The University of Texas System (US)
Corresponding author: Sharp, Paul M.
ORCID: Sharp, Paul M.
Li, Wen-Hsiung
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 1987
Volume: 15
Issue: 3
Pages: 1281-1295
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/15.3.1281
PMC: PMC340524
OpenAlex: W2018590530
Cited by: 3,992
References: 30
Citations by year: 2026: 223 · 2025: 203 · 2024: 205 · 2023: 177 · 2022: 198 · 2021: 239 · 2020: 212 · 2019: 147 · 2018: 155 · 2017: 120 · 2016: 133 · 2015: 112 · 2014: 147 · 2013: 145 · 2012: 137
FWCI: 7.58
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Nucleic Acids Research (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
Funders: National Institutes of Health
National Institute of General Medical Sciences (GM30998)
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 › Genetics › Evolution and Genetic Dynamics
Keywords: codon adaptation index, codon usage bias, codon usage, gene expression prediction, heterologous expression, highly expressed genes, natural selection
MeSH terms: Animals, Base Sequence, Cattle, Codon, Escherichia coli, Biological Evolution, Genes, Genes, Bacterial, Genes, Fungal, Humans, Mathematics, Models, Genetic, RNA, Messenger, Saccharomyces cerevisiae

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The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications

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