wSet: Codon Adaptation Index (CAI) w tables

In GeneGA: Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm

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.

Details

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

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.

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)

Example output

Loading required package: seqinr
Loading required package: hash
hash-3.0.1 provided by Decision Patterns

GeneGA documentation built on Nov. 8, 2020, 8:17 p.m.