nc.f {tAI} | R Documentation |
Nc vs. GC3s
Description
Calculates the expected Nc value of a gene for a given GC content at the third codon positions.
Usage
nc.f(x)
Arguments
x |
a vector of GC contents at third codon positions |
Details
Without selection on codon bias, the expected value of Nc as a function of GC content at third positions, x, is given by
f(x) = -6 + x + 34/(x^2 + (1.025 - x)^2).
This equation follows dos Reis et al. (2004, see also Wright 1990 for the original).
Value
A vector of Nc values for the given GC contents.
Author(s)
Mario dos Reis
References
Wright F. (1990) The 'effective number of codons' used in a gene. Gene, 87: 23–9.
dos Reis M., Savva R., and Wernisch L. (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res., 32: 5036–44.
Examples
curve(nc.f(x), xlab="GC3s content", ylab="Nc")
points(ecolik12$w$GC3s, ecolik12$w$Nc, pch=19)
[Package tAI version 0.2.2 Index]