Selected article for: "codon usage and Methods Materials"
Author: James T. Van Leuven; Martina M. Ederer; Katelyn Burleigh; LuAnn Scott; Randall A. Hughes; Vlad Codrea; Andrew D. Ellington; Holly Wichman; Craig Miller
Title: FX174 Attenuation by Whole Genome Codon Deoptimization
  • Document date: 2020_2_11
    • ID: mpb4fy16_11
    Snippet: other ΦX174 genes fall within this range of recoding. We calculated additional metrics of codon adaptation including an alternative version of CAI (81) , tRNA adaptation index: tAI (82) , index of translation elongation: I TE (83) , relative codon adaptation: RCA (84) , the number of effective codons: Nc (85) , and the starvation codon adaptation index: sCAI (86) . Nc differs from the other indices in that it measures the deviation from uniform .....
    Document: other ΦX174 genes fall within this range of recoding. We calculated additional metrics of codon adaptation including an alternative version of CAI (81) , tRNA adaptation index: tAI (82) , index of translation elongation: I TE (83) , relative codon adaptation: RCA (84) , the number of effective codons: Nc (85) , and the starvation codon adaptation index: sCAI (86) . Nc differs from the other indices in that it measures the deviation from uniform codon usage and does not score codon preference. The other indices compare the codon usage of any given gene to a set of genes that are known to be highly expressed in a cell. These latter indices differ from one another in how codon optimality is scored ( e.g. taking into account tRNA gene abundances). Calculation details are in the Materials and Methods. All analyses produced qualitatively similar rank-orders for ΦX174 genes (supplementary table S1).

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