cai: Codon adaptation index
In HVoltBb/kondonz: A Comprehensive Codon Analysis Toolbox

Description Usage Arguments Details Value Source References

Calculates the codon adaptation index (CAI) for each codon

1 2	cai(x, ref_spp = "n", ref, y = 0, threthold = 0.005, lower_bound = 0.005)

`x`	a KZsqns object, for which CAI will be calculated
`ref_spp`	a char sequence of species name to use. "ecoli" = Escherichia coli; "bsubt" = Bacillus subtilis; "scere" = Saccharomyces cerevisiae; When specified, it overides the value set by ref
`ref`	a named numeric array of relative adaptiveness (0 to 1) of each codon from a species-specific reference set of very highly expressed genes. The array should have a length of 64 with 0 filled in at the stop codons. The name of each number is the corresponding char array of codon. For example, "AAA" or "Aaa" represent the same codon. Upper case letters can be mixed with lower case letters.
`y`	an optional number denoting the codon table to be used. 0 = standard codon table (default), 2 = vertibrate mitchodrial (See dna2aa for additional options). When an option other than those mentioned above is provided, the standard codon table will be used
`threthold`	a number below which the adaptiveness will be forced to lower_bound
`lower_bound`	a number to which values of adaptiveness below the threshold will be forced

When any reference codon has a relative usage value of zero and the codon sequence to be calculated has such a codon, the CAI for this sequence would be zeroed out. lower_bound and threthold are there to prevent such an undesired result. There is a helper method cai_crt to calculate the reference table from a given reference set of highly expressed genes. It is the intention of the authors to keep this helper method seperate from the CAI method, and the user can device their own rules about how to construct a reference table by creating their own reference table or helper method.

a number denoting the CAI for the provided sequence

The reference set of very highly expressed genes for E. coli, B. subtilis and S. cerevisiae [1][2].

[1] Sharp, P. M., & Li, W.-H. (1986). Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare'codons. Nucleic acids research, 14(19), 7737-7749. [2] Shields, D. C., & Sharp, P. M. (1987). Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases. Nucleic acids research, 15(19), 8023-8040.

HVoltBb/kondonz documentation built on Jan. 11, 2020, 3:30 a.m.