Charge

charge - 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¶

Moore DS. Amino acid and peptide net charges: A simple calculational procedure. Biochem Educ. 13, 10-11 (1985).
http://emboss.sourceforge.net/apps/cvs/emboss/apps/iep.html

Examples¶

seq <- c("CARDRSTPWRRGIASTTVRTSW", "XXTQMYVRT") 
# Unnormalized charge
charge(seq)

[1] 3.9266889 0.9980008

# Normalized charge
charge(seq, normalize=TRUE)

[1] 0.1784859 0.1425715


# 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)

[1] 3.8946562 0.9977872