Codon usage

Description

aminoacyl is a list containing the codon counts of 36 genes encoding yeast aminoacyl-tRNA-synthetase(S.Cerevisiae).

Usage

data(aminoacyl)

Format

aminoacyl is a list containing the 5 following objects:

genes

is a vector giving the gene names.

localisation

is a vector giving the cellular localisation of the proteins (M = mitochondrial, C = cytoplasmic, I = indetermined, CI = cyto and mito).

codon

is a vector containing the 64 triplets.

AA

is a factor giving the amino acid names for each codon.

usage.codon

is a dataframe containing the codon counts for each gene.

Source

Data prepared by D. Charif Delphine.Charif@versailles.inra.fr starting from:
http://www.expasy.org/sprot/

References

Chiapello H., Olivier E., Landes-Devauchelle C., Nitschké P. and Risler J.L (1999) Codon usage as a tool to predict the cellular localisation of eukariotic ribosomal proteins and aminoacyl-tRNA synthetases. Nucleic Acids Res., 27, 14, 2848–2851.

Examples

data(aminoacyl)
aminoacyl$genes
aminoacyl$usage.codon
dudi.coa(aminoacyl$usage.codon, scannf = FALSE)