hmm_cc {protHMM}

hmm_cc

Description

The feature calculates the covariance between different residues separated along the protein sequences by a lag value across different amino acid emission frequency columns.

Usage

hmm_cc(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 x 19 x the lag value; by default this is a vector of length 1520.

Note

The lag value must less than the length of the amino acid 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_cc(system.file("extdata", "1DLHA2-7", package="protHMM"))