R: Calculates the net charge of amino acid sequences.

charge {alakazam} | R Documentation

## 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. http://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)

[Package alakazam version 0.3.0 Index]