seqinr (version 3.4-5)

caitab: Codon Adaptation Index (CAI) w tables

Description

Information about a preferred set of codons for highly expressed genes in three species.

Usage

data(caitab)

Format

A data frame with 64 rows for the codons and the following 3 columns:

ec

Escherichia coli

bs

Bacillus subtilis

sc

Saccharomyces cerevisiae

Details

Codons are given by row.names(caitab).

References

Sharp, P.M., Li, W.-H. (1987) The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research, 15:1281-1295.

Shields, D.C., Sharp, P.M. (1987) Synonymous codon usage in Bacillus subtilis reflects both traditional selection and mutational biases. Nucleic Acids Research, 15:8023-8040.

Sharp, P. M., Cowe, E. (1991). Synonymous codon usage in Saccharomyces cerevisiae. Yeast, 7:657-678.

Peden, J.F. (1999) Analysis of codon usage. PhD Thesis, University of Nottingham, UK.

citation("seqinr")

See Also

cai for an example using this dataset to compute CAI values.

Examples

# NOT RUN {
  data(caitab)
# }