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Cited by 68RNA and protein synthesis mechanismsGenomics and Phylogenetic StudiesEvolution and Genetic Dynamics

Relative Codon Adaptation Index, a Sensitive Measure of Codon Usage Bias

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Lee, Soohyun, Weon, Seyeon, Lee, Sooncheol, Kang, Changwon·2010·Evolutionary Bioinformatics
DOI 10.4137/ebo.s4608PMC PMC2880845
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Abstract

We propose a simple, sensitive measure of synonymous codon usage bias, the Relative Codon Adaptation Index (rCAI), as a way to discriminate better between highly biased and unbiased regions, compared with the widely used Codon Adaptation Index (CAI). CAI is a geometric mean of the relative usage of codons in a gene, and is calculated using the codon usage table trained with a set of highly expressed genes. In contrast, rCAI is computed by subtracting the background codon usage trained with two noncoding frames of highly expressed genes from the codon usage in the coding frame. rCAI has higher signal-to-noise ratio than CAI, considering that noncoding frames would not show codon bias. Translation efficiency and protein abundance correlates comparably or better with rCAI than CAI or other measures such as ‘effective number of codons’ and ‘SCUMBLE offsets’. Within overlapping coding regions, one of the two coding frames dominates in codon usage bias according to rCAI. Presumably, rCAI could substitute CAI in diverse applications.

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  • The frequencies of the peptides displayed on phages are not even in the library.

    “Usually, the frequencies of the peptides displayed on phages are not even in the library. There were some reasons for the heterogenous phage amount, such as biases in library construction, variance in the use of cryptography,45,46 the different growth rates of phages and peptide degradation by protease.47”

    From Identification of heptapeptides targeting a lethal bacterial strain in septic mice through an integrative approach (2022) · cites this paper as [46]

    The Results and Discussion section discusses codon usage in bacteriophage λ genes, not the frequencies of peptides displayed in a phage library. A search for phage-display library abundance and uneven peptide frequencies found no passage addressing the claim. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

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Authors
Lee, S., Weon, S., Lee, S., & Kang, C.
Affiliations
Korea Advanced Institute of Science and Technology (KR)
Corresponding author
Kang, Changwon
ORCID
Venue
Evolutionary Bioinformatics
Publisher
SAGE Publications
Published
2010-01
Volume
6
Pages
47-55
ISSN
1176-9343 (ISSN-L)
DOI
10.4137/ebo.s4608
PMC
PMC2880845
OpenAlex
W2082607332
Cited by
68
References
2
Citations by year
2026: 2 · 2025: 6 · 2024: 5 · 2023: 5 · 2022: 9 · 2021: 10 · 2020: 6 · 2019: 6 · 2018: 2 · 2017: 6 · 2016: 1 · 2015: 1 · 2014: 4 · 2013: 2 · 2012: 3
FWCI
0.65
Type
journal article
Language
en
Open access
Licence
Locations
  • Evolutionary Bioinformatics (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
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 usage bias, codon adaptation index, synonymous codons, translation efficiency, protein abundance, effective number of codons, signal-to-noise ratio

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