Strength of Selected Codon Usage
Description
The package can calculate the selection in codon usage in
bacteria species. First and most important, the package can
calculate the strength of selected codon usage bias (sscu)
based on Paul Sharp's method. The method take into account of
background mutation rate, and focus only on codons with
universal translational advantages in all bacterial species.
Thus the sscu index is comparable among different species. In
addition, detainled optimal codons (selected codons)
information can be calculated by optimal_codons function, so
the users will have a more accurate selective scheme for each
codons. Furthermore, we added one more function optimal_index
in the package. The function has similar mathematical formula
as s index, but focus on the estimates the amount of GC-ending
optimal codon for the highly expressed genes in the four and
six codon boxes. The function takes into account of background
mutation rate, and it is comparable with the s index. However,
since the set of GC-ending optimal codons are likely to be
different among different species, the index can not be
compared among different species.