R: Calculates the aliphatic index of amino acid sequences

aliphatic {alakazam} | R Documentation

## 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)

[Package alakazam version 0.3.0 Index]