many thanks for posting this interesting technical qestion on RG. I'm absolutely not a specialist in this field of research as we work in synthetic inorganic chemistry. However, I just came across the following potentially useful literature references:
FEGS: a novel feature extraction model for protein sequences and its applications
Article FEGS: a novel feature extraction model for protein sequences...
and
Feature extraction method for proteins based on Markov tripeptide by compressive sensing
Article Feature extraction method for proteins based on Markov tripe...
Fortunately both articles have been posted by the authors as public full texts. Thus these papers are freely available as pdf files. I'm sure that you will find other helpful articles when you search the "Publications" section of RG.
Good luck with your work and best wishes, Frank Edelmann