alakazam (version 1.3.0)

gravy: 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)

Value

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

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.

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)