CUB: Computes the Codon Usage Bias of DNA sequences

In vhica: Vertical and Horizontal Inheritance Consistence Analysis

Computes the Codon Usage Bias of DNA sequences

Description

The function reads aligned sequences in a fasta file and estimates the codon usage bias for each sequence. Several methods exist to estimate CUB; so far, only the "Effective Number of Codons" (ENC) calculation is available.

Usage

CUB(file = NULL, sequence = NULL, method = "ENC")

Arguments

file	FASTA file in which aligned sequences are stored.
sequence	Alternatively, the result of seqinr::read.fasta.
method	The method used to compute CUB. "ENC": Effective Number of Codons, as described in Wright (1990).

Value

A named vector of CUB scores. Names correspond to sequence names in the dataset.

Author(s)

Aurelie Hua-Van and Arnaud Le Rouzic.

References

Wright, F. (1990). The 'effective number of codons' used in a gene. Gene, 87(1), 23-29.

See Also

div

Examples

	seq.file <- system.file("extdata/Genes", "Amd.fas", package="vhica")
	CUB(seq.file)

vhica documentation built on March 31, 2023, 10:09 p.m.