aliphatic {alakazam}

Calculates the aliphatic index of amino acid sequences

Description

aliphatic calculates the aliphatic index of amino acid sequences using the method of Ikai. Non-informative positions are excluded, where non-informative is defined as any character in c("X", "-", ".", "*").

Usage

aliphatic(seq, normalize = TRUE)

Arguments

seq

vector of strings containing amino acid sequences.

normalize

if TRUE then divide the aliphatic index of each amino acid sequence by the number of informative positions. Non-informative position are defined by the presence any character in c("X", "-", ".", "*"). If FALSE then return the raw aliphatic index.

Value

A vector of the aliphatic indices for the sequence(s).

References

1. Ikai AJ. Thermostability and aliphatic index of globular proteins. J Biochem. 88, 1895-1898 (1980).

Examples

seq <- c("CARDRSTPWRRGIASTTVRTSW", NA, "XXTQMYVRT")
aliphatic(seq)