EXP: Vectors of coefficients to compute linear forms.
In seqinr: Biological Sequences Retrieval and Analysis

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).

Usage

data(EXP)

Format

List of 24 vectors of coefficients

A: num [1:4] 1 0 0 0
A3: num [1:64] 1 0 0 0 1 0 0 0 1 0 ...
AGZ: num [1:64] 0 0 0 0 0 0 0 0 1 0 ...
ARG: num [1:64] 0 0 0 0 0 0 0 0 1 0 ...
AU3: num [1:64] 1 0 0 1 1 0 0 1 1 0 ...
BC: num [1:64] 0 1 0 0 0 0 0 0 0 0 ...
C: num [1:4] 0 1 0 0
C3: num [1:64] 0 1 0 0 0 1 0 0 0 1 ...
CAI: num [1:64] 0.00 0.00 -1.37 -2.98 -2.58 ...
CG: num [1:4] 0 1 1 0
CG1: num [1:64] 0 0 0 0 0 0 0 0 0 0 ...
CG12: num [1:64] 0 0 0 0 0.5 0.5 0.5 0.5 0.5 0.5 ...
CG2: num [1:64] 0 0 0 0 1 1 1 1 1 1 ...
CG3: num [1:64] 0 1 1 0 0 1 1 0 0 1 ...
CGN: num [1:64] 0 0 0 0 0 0 0 0 0 0 ...
F1: num [1:64] 1.026 0.239 1.026 0.239 -0.097 ...
G: num [1:4] 0 0 1 0
G3: num [1:64] 0 0 1 0 0 0 1 0 0 0 ...
KD: num [1:64] -3.9 -3.5 -3.9 -3.5 -0.7 -0.7 -0.7 -0.7 -4.5 -0.8 ...
Q: num [1:64] 0 0 0 0 1 1 1 1 0 0 ...
QA3: num [1:64] 0 0 0 0 1 0 0 0 0 0 ...
QC3: num [1:64] 0 0 0 0 0 1 0 0 0 0 ...
U: num [1:4] 0 0 0 1
U3: num [1:64] 0 0 0 1 0 0 0 1 0 0 ...

Details

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)).

Source

ANALSEQ EXPFILEs for command EXP.
http://pbil.univ-lyon1.fr/software/doclogi/docanals/manuel.html

References

citation("seqinr")

A: content in A nucleotide
A3: 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