hmm_SepDim: hmm_SepDim

In protHMM: Protein Feature Extraction from Profile Hidden Markov Models

hmm_SepDim

Description

This feature calculates the probabilistic expression of amino acid dimers that are spatially separated by a distance l. Mathematically, this is done with a 20 x 20 matrix F, in which F[m, n] = \sum_{i = 1}^{L-l} H_{i, m}H_{i+k, n}. H corresponds to the original HMM matrix, and L is the number of rows in H. Matrix F is then flattened to a feature vector of length 400, and returned.

Usage

hmm_SepDim(hmm, l = 7)

Arguments

hmm	The name of a profile hidden markov model file.
l	Spatial distance between dimer residues.

Value

A vector of length 400

References

Saini, H., Raicar, G., Sharma, A., Lal, S. K., Dehzangi, A., Lyons, J., Paliwal, K. K., Imoto, S., & Miyano, S. (2015). Probabilistic expression of spatially varied amino acid dimers into general form of Chou's pseudo amino acid composition for protein fold recognition. Journal of Theoretical Biology, 380, 291–298.

Examples

h<- hmm_SepDim(system.file("extdata", "1DLHA2-7", package="protHMM"))

protHMM documentation built on July 9, 2023, 6:10 p.m.