GenomicSig (version 0.1.0)

AminoAcidContent: Amino Acid Content

Description

Amino acid content refers to the relative frequencies of amino acids used in a protein or a proteome with 20 different amino acids as 20 dimensional vectors.

Usage

AminoAcidContent(fasta_file, type = c("DNA", "protein"))

Value

This function returns a data frame containing the sequence identifier fetched from the input fasta file and amino acid content of that sequence.

Arguments

fasta_file

Path of a fasta file containing nucleotide or protein sequence.

type

Type of the sequence, can be either "DNA" or "protein".

Author

Dr. Anu Sharma, Megha Garg

Details

Amino acid content refers to the relative frequencies of amino acids in the protein.If DNA sequence is given as input, it will be translated to a protein sequence. Then amino acid content will be calculated.

References

Sandberg, R., Bränden, C. I., Ernberg, I., & Cöster, J. (2003). Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+ C content. Gene, 311, 35-42.

Xiao, N., Cao, D. S., Zhu, M. F., & Xu, Q. S. (2015). protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences. Bioinformatics, 31(11), 1857-1859.

Examples

library(GenomicSig)
AminoAcidContent(fasta_file= system.file("extdata/Nuc_sequence.fasta", package = "GenomicSig"),
type = "DNA")
AminoAcidContent(fasta_file= system.file("extdata/prot_sequence.fasta", package = "GenomicSig"),
type = "protein")