sscu-package

The package sscu (Strength of Selected Codon Usage) calculates the selective profile in codon usage in bacteria species. First of all, the package calculate the s index 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 s index is comparable among different species. In addition, detailed 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.

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.

sscu-package: Strength of Selected Codon Usage

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References