sscu - Strength of Selected Codon Usage
The package calculates the indexes for selective stength
in codon usage in bacteria species. (1) The package can
calculate the strength of selected codon usage bias (sscu, also
named as s_index) based on Paul Sharp's method. The method take
into account of background mutation rate, and focus only on
four pairs of codons with universal translational advantages in
all bacterial species. Thus the sscu index is comparable among
different species. (2) The package can detect the strength of
translational accuracy selection by Akashi's test. The test
tabulating all codons into four categories with the feature as
conserved/variable amino acids and optimal/non-optimal codons.
(3) Optimal codon lists (selected codons) can be calculated by
either op_highly function (by using the highly expressed genes
compared with all genes to identify optimal codons), or
op_corre_CodonW/op_corre_NCprime function (by correlative
method developed by Hershberg & Petrov). Users will have a list
of optimal codons for further analysis, such as input to the
Akashi's test. (4) The detailed codon usage information, such
as RSCU value, number of optimal codons in the highly/all gene
set, as well as the genomic gc3 value, can be calculate by the
optimal_codon_statistics and genomic_gc3 function. (5)
Furthermore, we added one test function low_frequency_op in the
package. The function try to find the low frequency optimal
codons, among all the optimal codons identified by the
op_highly function.