GeneGA (version 1.22.0)

wSet: Codon Adaptation Index (CAI) w tables

Description

Codon Adaptation Index (CAI) w tables of almost 200 genomes,the computation is based on the highly expressed genes of these genomes.

Usage

data(wSet)

Format

A data frame with 200 observations on the following 64 variables, which denote the 64 codes.

Source

The data were combined from two sources: the first part is the first three rows,which contains w tables masked from the caitab dataset of seqinr package,while the other 197 rows were computed based the predicted highly expressed genes of 197 genomes from HEG-DB database.

Details

Codons can be accessed by names(wSet) and the genome names can be accessed by row.names(wSet).

References

Puigbo P, Romeu A, Garcia-Vallve S. HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. Nucl. Acids Res. 2008, 36:D524-527.

Charif D, Lobry J. 2007. SeqinR 1.0-2. A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis. In: Structural Approaches to Sequence Evolution (Bastolla U, Porto M, Roman E, Vendruscolo M, eds.), Berlin Heidelberg: Springer, p207-232.

See Also

GeneCodon, GeneGA, GeneFoldGA

Examples

data(wSet)