aliphatic - Calculates the aliphatic index of amino acid sequences
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", "-", ".", "*").
aliphatic(seq, normalize = TRUE)
- vector of strings containing amino acid sequences.
TRUEthen 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
FALSEthen return the raw aliphatic index.
A vector of the aliphatic indices for the sequence(s).
- Ikai AJ. Thermostability and aliphatic index of globular proteins. J Biochem. 88, 1895-1898 (1980).
seq <- c("CARDRSTPWRRGIASTTVRTSW", NA, "XXTQMYVRT") aliphatic(seq)
 0.4000000 NA 0.4142857