alakazam (version 1.2.1)

polar: 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)

Value

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

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.

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)