sscu

This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see sscu.

Strength of Selected Codon Usage

Bioconductor version: 3.3

The package can calculate the selection in codon usage in bacteria species. First and most important, the package can calculate the strength of selected codon usage bias (sscu) based on Paul Sharp's method. The method take into account of background mutation rate, and focus only on codons with universal translational advantages in all bacterial species. Thus the sscu index is comparable among different species. In addition, detainled optimal codons (selected codons) information can be calculated by optimal_codons function, so the users will have a more accurate selective scheme for each codons. Furthermore, we added one more function optimal_index in the package. The function has similar mathematical formula as s index, but focus on the estimates the amount of GC-ending optimal codon for the highly expressed genes in the four and six codon boxes. The function takes into account of background mutation rate, and it is comparable with the s index. However, since the set of GC-ending optimal codons are likely to be different among different species, the index can not be compared among different species.

Author: Yu Sun

Maintainer: Yu Sun <sunyu1357 at gmail.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("sscu")

Documentation

Details

Package Archives

Follow Installation instructions to use this package in your R session.