get.tai: The tRNA adaptation index
In mariodosreis/tai: The tRNA adaptation index

Description Usage Arguments Details Value Author(s) References See Also Examples

Calculates the tRNA adaptation index (tAI) of dos Reis et al. (2003, 2004).

1	get.tai(x, w)

`x`	an n by 60 matrix of codon frequencies for n open reading frames.
`w`	a vector of length 60 of relative adaptiveness values for codons.

The tRNA adaptation index (tAI) is a measure of the level of co-adaptation between the set of tRNA genes and the codon usage bias of protein-coding genes in a given genome. STOP and methionine codons are ignored. The standard genetic code is assumed.

A vector of length n of tAI values.

Mario dos Reis

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.

get.ws

# Calculate relative adaptiveness values (ws) for E. coli K-12
eco.ws <- get.ws(tRNA=ecolik12$trna, sking=1)

# Calculate tAI for a set of 49 E. coli K-12 coding genes
eco.tai <- get.tai(ecolik12$m[,-33], eco.ws)

# Plot tAI vs. effective number of codons (Nc)
plot(eco.tai, ecolik12$w$Nc, xlab="tAI", ylab="Nc")