Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences

Bahir, Iris; Fromer, Menachem; Prat, Yosef; Linial, Michal

Divergence between the codon usage of two viruses, two hosts, or virus and host was estimated according to the distances between their usage vectors. Specifically, for each group, a usage vector of 59 coordinates, denoted as F¼(f 1 ,y,f 59 ), was calculated as described above. The distance between two such vectors was measured in two q . For differences in the amino acid frequencies between two species, the same method was used, with the corresponding 20-coordinated vectors. The codon usage differences were also measured in a manner that integrates the amino acid frequencies, where the 59 codons were assigned their empirical frequencies in the data, regardless of their corresponding amino acid frequency. This quantification results in a probability vector P¼(p 1 ,y,p 59 ), where P 59 i¼1 p i ¼ 1.