R: Vectors of coefficients to compute linear forms.
EXP
R Documentation
Vectors of coefficients to compute linear forms.
Description
This dataset is used to compute linear forms on codon frequencies:
if codfreq is a vector of codon frequencies then
drop(freq %*% EXP$CG3) will return for instance the G+C content
in third codon positions. Base order is the lexical order: a,
c, g, t (or u).
It's better to work directly at the amino-acid level
when computing linear forms on amino-acid frequencies so as to have
a single coefficient vector. For instance EXP$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)).
content in A nucleotide in third position of codon
AGZ
Arg content (aga and agg codons)
ARG
Arg content
AU3
content in A and U nucleotides in third position of codon
BC
Good choice (Bon choix). Gouy M., Gautier C. (1982)
codon usage in bacteria : Correlation with gene expressivity. Nucleic Acids Research,10(22):7055-7074.
C
content in C nucleotides
C3
content in A nucleotides in third position of codon
CAI
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.
CG
content in G + C nucleotides
CG1
content in G + C nucleotides in first position of codon
CG12
content in G + C nucleotides in first and second position of codon
CG2
content in G + C nucleotides in second position of codon
CG3
content in G + C nucleotides in third position of codon
CGN
content in CGA + CGU + CGA + CGG
F1
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.
G3
content in G nucleotides in third position of codon
KD
Kyte, J., Doolittle, R.F. (1982) A simple method for displaying
the hydropathic character of a protein. J. Mol. Biol.,157
:105-132.
Q
content in quartet
QA3
content in quartet with the A nucleotide in third position
QC3
content in quartet with the A nucleotide in third position
U
content in U nucleotide
U3
content in U nucleotides in third position of codon