R: Calculates the hydrophobicity of amino acid sequences

gravy {alakazam} | R Documentation

## Calculates the hydrophobicity of amino acid sequences

### Description

`gravy` calculates the Grand Average of Hydrophobicity (GRAVY) index of amino acid sequences using the method of Kyte & Doolittle. Non-informative positions are excluded, where non-informative is defined as any character in `c("X", "-", ".", "*")`.

### Usage

    gravy(seq, hydropathy = NULL)

### Arguments

`seq` | vector of strings containing amino acid sequences.
`hydropathy` | named numerical vector defining hydropathy index values for each amino acid, where names are single-letter amino acid character codes. If `NULL`, then the Kyte & Doolittle scale is used.

### Value

A vector of GRAVY scores for the sequence(s).

### References

1. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 157, 105-32 (1982).

### See Also

For additional hydrophobicity indices see `aaindex`.

### Examples

    # Default scale
    seq <- c("CARDRSTPWRRGIASTTVRTSW", "XXTQMYVRT")
    gravy(seq)

    # Use the Kidera et al, 1985 scores from the seqinr package
    library(seqinr)
    data(aaindex)
    x <- aaindex[["KIDA850101"]]$I
    # Rename the score vector to use single-letter codes
    names(x) <- translateStrings(names(x), ABBREV_AA)
    # Calculate hydrophobicity
    gravy(seq, hydropathy=x)

[Package alakazam version 0.3.0 Index]