Calculates the aliphatic index of amino acid sequences

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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

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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

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

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