GC_content: GC content of nucleic acid sequences

In GenomicSig: Computation of Genomic Signatures

GC content of nucleic acid sequences

Description

This function calculates the percentage of guanine (G) or cytosine (C) nitrogenous bases in a DNA or RNA molecule. This measure indicates the proportion of G and C bases out of an implied four total bases, which including adenine (A) and thymine (T) in DNA. And adenine and uracil (U) in RNA along with G and C.

Usage

GC_content(sequence)

Arguments

sequence

Input as a nucleic acid sequence of characters from fasta file.

Details

G+C content is estimated with ambiguous bases taken into account.

Value

This function returns the fraction of G+C as a numeric vector of length one for all sequences.

Author(s)

Dr. Anu Sharma, Dr. Girish Kumar Jha

References

Nakabachi, A., Yamashita, A., Toh, H., Ishikawa, H., Dunbar, H. E., Moran, N. A., & Hattori, M. (2006). The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science, 314(5797), 267-267.

Barbu, E., Lee, K. Y., & Wahl, R. (1956, August). Content of purine and pyrimidine base in desoxyribonucleic acid of bacteria. In Annales de l'Institut Pasteur (Vol. 91, No. 2, p. 212).

Examples

library(GenomicSig)
GC_content(sequence = system.file("extdata/Nuc_sequence.fasta", package = "GenomicSig"))

GenomicSig documentation built on Sept. 11, 2024, 6:19 p.m.