bulk {alakazam}

Calculates the average bulkiness of amino acid sequences

Description

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

Usage

bulk(seq, bulkiness = NULL)

Arguments

seq

vector of strings containing amino acid sequences.

bulkiness

named numerical vector defining bulkiness scores for each amino acid, where names are single-letter amino acid character codes. If NULL, then the Zimmerman et al, 1968 scale is used.

Value

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

References

1. Zimmerman JM, Eliezer N, Simha R. The characterization of amino acid sequences in proteins by statistical methods. J Theor Biol 21, 170-201 (1968).

See Also

For additional size related indices see aaindex.

Examples

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

# Use the Grantham, 1974 side chain volumn scores from the seqinr package
library(seqinr)
data(aaindex)
x <- aaindex[["GRAR740103"]]$I
# Rename the score vector to use single-letter codes
names(x) <- translateStrings(names(x), ABBREV_AA)
# Calculate average volume
bulk(seq, bulkiness=x)