Among the reasons he offers are software complexity, nearly infinite variations of usage scenarios, many different user interfaces and operating environments and a lack of time and resources to test everything.
COA of codon usage was used to study extensively and quantitatively the variation of codon usage among the 1180 genes on the chromosome.
Furthermore, the combined effect of mutational pressure and natural selection on influencing codon usage patterns of viruses is substantial (explaining 10% and 8% of total variation of codon usage patterns).
A correspondence analysis on the relative synonymous codon usage (RSCU) values using the software CodonW [ 63] was performed to examine the variation of codon usage among genes.
Figures 5a through c show that the variation of resource usage is more uniformly distributed in the coordinated provisioning approach when compared to its non-coordinated counterpart.
Since middle poly(A) sites are usually less frequently used than proximal and distal sites [16], [41], variation of their usage would have only a marginal effect, if any, on median-based sample RUD and detection of global trend of 3'UTR lengthening or shortening.
The variation of codon usage among genes was explored using the correspondence analysis tool within CodonW.
Complex factors are found to be responsible for variation of codon usage in L. intracellularis chromosome.
Based on the above narration, the variation of codon usage of genes within a species is due to the combined effect of mutation and selection.
