To run the model, you are requested to thorughly follow the listed steps:
01. Convert elm to .csv:
    Run "Pre-processing.ipynb(.elm to .csv)" with proper function parameters (input is the .elm file downloaded from "http:https://plmd.biocuckoo.org/download.php"
    Extract the sequences with proper window size to get-
    > MethylationPositive.txt
    > MethylationnNegative.txt

02. Get proteins in fasta format:
    Run "ConvertFASTA.py" with proper function parameters (input is the output from previous step)
    > python ConvertFASTA.py myfile.txt result.fasta

03. CD_HIT to eliminate identical proteins over negative sequence only:
    Run "run-1595357618.sh" CDHIT (http:https://weizhong-lab.ucsd.edu/cdhit_suite/cgi-bin/index.cgi?cmd=cd-hit)
To get the fasta sequence in different files for getting PSSM

04. Get All PSSMs
    Run PSSM on the NCBI local blast tool using the "pssm_commands.m" file commands
    > makeblastdb -in sequence.fsa -dbtype prot -parse_seqids -out newdatabase -title "newdb"
    > psiblast -query sequence.fsa -db newdatabase -num_iterations=3 -evalue=0.001 -pseudocount=1 -out psiblastOut.txt -out_ascii_pssm=PSSM -save_each_pssm

05. Get All SPD2
# By given protein sequences in fasta format, you can run command
> ../misc/run_local.sh *.seq
to obtain predicted secondary structure, ASA, backbone torsion angles.
## If you already have pssm files for your proteins.
> ../misc/pred_pssm.py *.pssm
The output will be seen in *.spd3    

06. Get Total Features
    Run "vectorgenerate.py" to get the total features

07. Get Model Performance Statistics
    Run "MeSEP.py" to get number of Kmeth sites and non-Kmeth sites