get.ws: Relative adaptiveness values

In mariodosreis/tai: The tRNA adaptation index

Relative adaptiveness values

Description

Calculates the relative adaptiveness values of codons based on the number of tRNA genes.

Usage

get.ws(tRNA, s = NULL, sking)

Arguments

tRNA	a vector of length 64 with tRNA gene copy numbers
s	a vector of length 9 with selection penalties for codons
sking	a vector of length 1 indicating the superkingdom

Details

The relative adaptiveness values are calculated as described in dos Reis et al. (2003, 2004). If s = NULL, the s values are set to the optimised values of dos Reis et al. (2004). sking indicates the superkingdom, with 0 indicating Eukaryota, and 1 Prokaryota.

Value

A vector of length 60 of relative adaptiveness values.

Author(s)

Mario dos Reis

References

dos Reis M., Wernisch L., and Savva R. (2003) Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Res., 31: 6976–85.

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

eco.ws <- get.ws(tRNA=ecolik12$trna, sking=1)

mariodosreis/tai documentation built on June 9, 2022, 7:37 p.m.