Evolution of Viral Proteins Originated De Novo by Overprinting

Sabath, Niv; Wagner, Andreas; Karlin, David

3) The CSI of the overlapping regions relative to protein coding genes in the rest of the genome. CSI is based on the algorithm used to calculate the CAI (Sharp and Li 1987) , which is the most commonly used measure of codon usage bias. The CAI compares the codon usage of a gene with that of a reference set of highly expressed genes in a given genome to examine whether a protein-coding gene is subject to selection for high translation rate (and thus presumably highly expressed). Instead, in this study, we apply the CSI as a measure of the similarity between the codon usage of a gene and that of all other genes in the same genome. Therefore, we calculated the CSI of a given gene as described in Sharp and Li (1987) with the difference that the reference used was the codon usage of all other protein-coding genes in the same genome instead of the codon usage only of highly expressed genes. We performed this calculation for the overlapping regions of all 12 ancestral/de novo gene pairs. Note that unlike relative divergence and selective constraint, the CSI is calculated for single genes and not for pairs of homologous genes.