polar {alakazam}

Calculates the average polarity of amino acid sequences

Description

polar calculates the average polarity score of amino acid sequences. Non-informative positions are excluded, where non-informative is defined as any character in c("X", "-", ".", "*").

Usage

polar(seq, polarity = NULL)

Arguments

seq

vector of strings containing amino acid sequences.

polarity

named numerical vector defining polarity scores for each amino acid, where names are single-letter amino acid character codes. If NULL, then the Grantham, 1974 scale is used.

Value

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

References

1. Grantham R. Amino acid difference formula to help explain protein evolution. Science 185, 862-864 (1974).

See Also

For additional size related indices see aaindex.

Examples

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

# Use the Zimmerman et al, 1968 polarity scale from the seqinr package
library(seqinr)
data(aaindex)
x <- aaindex[["ZIMJ680103"]]$I
# Rename the score vector to use single-letter codes
names(x) <- translateStrings(names(x), ABBREV_AA)
# Calculate polarity
polar(seq, polarity=x)