alakazam (version 1.3.0)

aliphatic: 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)

Value

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

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.

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)