alakazam (version 1.2.1)

bulk: 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)

Value

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

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.

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)