find_nhc {signalHsmm}

Localize n-, h- and c-region in signal peptide

Description

Finds borders between distinct regions constituting signal peptides using a heuristic algorithm.

Usage

find_nhc(protein, signal = NULL)

Arguments

protein

a vector of amino acids or object of class SeqFastaAA.

signal

range of signal peptide. If NULL, the attribute sig of protein will be used.

Value

a vector of length 4 containing positions of:

1. start of n-region,

2. start of h-region,

3. start of c-region,

4. cleavage site.

References

Henrik Nielsen, Anders Krogh (1998). Prediction of signal peptides and signal anchors by a hidden Markov model. Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology.