hmm_ac {protHMM}

hmm_ac

Description

This feature calculates the covariance between two residues separated by a lag value within the same amino acid emission frequency column along the protein sequence.

Usage

hmm_ac(hmm, lg = 4)

Arguments

hmm

The name of a profile hidden markov model file.

lg

The lag value, which indicates the distance between residues.

Value

A vector of length 20 \times the lag value; by default this is a vector of length 80.

Note

The lag value must be less than the length of the protein sequence

References

Dong, Q., Zhou, S., & Guan, J. (2009). A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation. Bioinformatics, 25(20), 2655–2662.

Examples

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