This dataset is used to compute linear forms on codon frequencies:
if codfreq is a vector of codon frequencies then
drop(freq %*% EXP$CG3) will return for instance the G+C content
in third codon positions. Base order is the lexical order: a,
c, g, t (or u).
data(EXP)List of 24 vectors of coefficients
num [1:4] 1 0 0 0
num [1:64] 1 0 0 0 1 0 0 0 1 0 ...
num [1:64] 0 0 0 0 0 0 0 0 1 0 ...
num [1:64] 0 0 0 0 0 0 0 0 1 0 ...
num [1:64] 1 0 0 1 1 0 0 1 1 0 ...
num [1:64] 0 1 0 0 0 0 0 0 0 0 ...
num [1:4] 0 1 0 0
num [1:64] 0 1 0 0 0 1 0 0 0 1 ...
num [1:64] 0.00 0.00 -1.37 -2.98 -2.58 ...
num [1:4] 0 1 1 0
num [1:64] 0 0 0 0 0 0 0 0 0 0 ...
num [1:64] 0 0 0 0 0.5 0.5 0.5 0.5 0.5 0.5 ...
num [1:64] 0 0 0 0 1 1 1 1 1 1 ...
num [1:64] 0 1 1 0 0 1 1 0 0 1 ...
num [1:64] 0 0 0 0 0 0 0 0 0 0 ...
num [1:64] 1.026 0.239 1.026 0.239 -0.097 ...
num [1:4] 0 0 1 0
num [1:64] 0 0 1 0 0 0 1 0 0 0 ...
num [1:64] -3.9 -3.5 -3.9 -3.5 -0.7 -0.7 -0.7 -0.7 -4.5 -0.8 ...
num [1:64] 0 0 0 0 1 1 1 1 0 0 ...
num [1:64] 0 0 0 0 1 0 0 0 0 0 ...
num [1:64] 0 0 0 0 0 1 0 0 0 0 ...
num [1:4] 0 0 0 1
num [1:64] 0 0 0 1 0 0 0 1 0 0 ...
It's better to work directly at the amino-acid level
when computing linear forms on amino-acid frequencies so as to have
a single coefficient vector. For instance EXP$KD to compute the Kyte
and Doolittle hydrophaty index from codon frequencies is valid only
for the standard genetic code.
An alternative for drop(freq %*% EXP$CG3) is
sum( freq * EXP$CG3 ), but this is less efficient in terms of CPU
time. The advantage of the latter, however, is that thanks to
recycling rules you can use either sum( freq * EXP$A )
or sum( freq * EXP$A3 ). To do the same with the %*%
operator you have to explicit the recycling rule as in
drop( freq %*% rep(EXP$A, 16)).
citation("seqinr")
content in A nucleotide
content in A nucleotide in third position of codon
Arg content (aga and agg codons)
Arg content
content in A and U nucleotides in third position of codon
Good choice (Bon choix). Gouy M., Gautier C. (1982) codon usage in bacteria : Correlation with gene expressivity. Nucleic Acids Research,10(22):7055-7074.
content in C nucleotides
content in A nucleotides in third position of codon
Codon adaptation index for E. coli. Sharp, P.M., Li, W.-H. (1987) The codon adaptation index - a measure of directionam synonymous codon usage bias, and its potential applications. Nucleic Acids Research,15:1281-1295.
content in G + C nucleotides
content in G + C nucleotides in first position of codon
content in G + C nucleotides in first and second position of codon
content in G + C nucleotides in second position of codon
content in G + C nucleotides in third position of codon
content in CGA + CGU + CGA + CGG
From Table 2 in Lobry, J.R., Gautier, C. (1994) Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encode genes. Nucleic Acids Research,22:3174-3180.
content in G nucleotides in third position of codon
Kyte, J., Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol.,157 :105-132.
content in quartet
content in quartet with the A nucleotide in third position
content in quartet with the A nucleotide in third position
content in U nucleotide
content in U nucleotides in third position of codon