charge - Calculates the net charge of amino acid sequences.
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.
charge(seq, pH = 7.4, pK = NULL, normalize = FALSE)
- vector strings defining of amino acid sequences.
- environmental pH.
- 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.
TRUEthen 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
FALSEthen return the raw net charge.
A vector of net charges for the sequence(s).
- Moore DS. Amino acid and peptide net charges: A simple calculational procedure. Biochem Educ. 13, 10-11 (1985).
seq <- c("CARDRSTPWRRGIASTTVRTSW", "XXTQMYVRT") # Unnormalized charge charge(seq)
 3.9266889 0.9980008
# Normalized charge charge(seq, normalize=TRUE)
 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)
 3.8946562 0.9977872
For additional pK scales see