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_56
Snippet: Calculations of genome statistics were done as follows: Codon Adaptation Index (CAI) was calculated using the seqinr cai() function in R which uses the Sharp and Li 1987 method and the E. coli codon usage table. An alternative form of CAI was also calculated using an updated method outlined in Xia 2007. The number of effective codons (Nc) was calculated following (85) ......
Document: Calculations of genome statistics were done as follows: Codon Adaptation Index (CAI) was calculated using the seqinr cai() function in R which uses the Sharp and Li 1987 method and the E. coli codon usage table. An alternative form of CAI was also calculated using an updated method outlined in Xia 2007. The number of effective codons (Nc) was calculated following (85) .
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