charge {alakazam}

Calculates the net charge of amino acid sequences.

Description

charge calculates the net charge of amino acid sequences using the method of Moore, 1985, with exclusion of the C-terminus and N-terminus charges.

Usage

charge(seq, pH = 7.4, pK = NULL, normalize = FALSE)

Arguments

seq

vector strings defining of amino acid sequences.

pH

environmental pH.

pK

named vector defining pK values for each charged amino acid, where names are the single-letter amino acid character codes c("R", "H", "K", "D", "E", "C", "Y")). If NULL, then the EMBOSS scale is used.

normalize

if TRUE then divide the net charge of each amino acid sequence by the number of informative positions. Non-informative position are defined by the presence any character in c("X", "-", ".", "*"). If FALSE then return the raw net charge.

Value

A vector of net charges for the sequence(s).

References

1. Moore DS. Amino acid and peptide net charges: A simple calculational procedure. Biochem Educ. 13, 10-11 (1985).

2. https://emboss.sourceforge.net/apps/cvs/emboss/apps/iep.html

See Also

For additional pK scales see pK.

Examples

seq <- c("CARDRSTPWRRGIASTTVRTSW", "XXTQMYVRT") 
# Unnormalized charge
charge(seq)
# Normalized charge
charge(seq, normalize=TRUE)

# Use the Murray et al, 2006 scores from the seqinr package
library(seqinr)
data(pK)
x <- setNames(pK[["Murray"]], rownames(pK))
# Calculate charge
charge(seq, pK=x)