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