Codon Adaptation Index (CAI) Analysis

Codon adaptation index (CAI) is a quantitative value that indicates how frequently a favored codon is used amongst highly expressed genes. It is a primary indicator of translation efficiency and is used to engineer nucleotide sequences to obtain maximal protein production for vaccine purposes (Gustafsson et al., 2012). CAI values range between 0.0 and 1.0; with higher values indicating a higher gene expression potential. Further, values close to 1 indicate that codons with higher RSCU values are being used in the gene. The CAI value is sequence length independent; this value depends only on the amino acid frequency (Xia, 2007). In the present work, CAI values were calculated for all nine CDSs of NiV individually, using an RSCU reference set for each organism.