Gravy

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)

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¶

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

Examples¶

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

[1] -0.9181818 -0.6571429


# 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)

[1] 0.3240909 0.3628571