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

  1. 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

See also

For additional hydrophobicity indices see [aaindex](http://www.rdocumentation.org/packages/seqinr/topics/aaindex).