caitab: Codon Adaptation Index (CAI) w tables

In seqinr: Biological Sequences Retrieval and Analysis

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).

Source

The data were hard-encoded in the C program codonW version 1.4.4 writen by John Peden available at https://codonw.sourceforge.net/. The data are from the file codonW.h. According to this source file, there were no reference for Escherichia coli and Bacillus subtilis and the reference for Saccharomyces cerevisiae was Sharp and Cowe (1991).

It turns out that the data for Escherichia coli and Saccharomyces cerevisiae are identical to table 1 in Sharp and Li (1987) where the missing values for the stop codons are represented here by zeros. All codons were documented by at least one count in both datasets.

The data for Bacillus subtilis are from table 2 in Shields and Sharp (1987). Missing values for stops codons are represented as previously by zeros, missing values for single-box amino-acids are represented by 1 here. Note that some codons were undocumented in this dataset and that a 0.5 value in absolute frequencies was already forced to avoid zeros. It is therefore impossible to use directly these data to obtain the exact expected CAI values as documented in cai because of overlapping with documented codons.

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

  data(caitab)

seqinr documentation built on March 31, 2023, 3:05 p.m.