Comparative context analysis of codon pairs on an ORFeome scale

Table 3 Ranking of the codon pairs that display the highest residual difference between S. cerevisiae, S. pombe and C. albicans

Anaconda was used to analyze the codon context of the complete genomes of S. cerevisiae, S. pombe and C. albicans. The adjusted residuals of each codon context calculated for each pair of genomes - that is, S. pombe-S. cerevisiae; S. pombe-C. albicans; and C. albicans-S. cerevisiae - were subtracted and the result converted into a positive number by a module calculation. These values were used to rank the respective codon contexts and the 10 highest cases obtained were selected. Among these three yeast species, S. pombe and S. cerevisiae display the lowest differences, with the maximum value of the difference being found for the CAG-CAG pair (27.798). For S. pombe and C. albicans that value reaches 100.639 for the CAA-CAA codon pair. It is noteworthy that the highest difference value for the former pair is lower than the lowest value for the latter in this ranking of context differences. The only codon pair shared between all three yeast pairs is shown in bold.

ISSN: 1474-760X