I successfully got the gff with the methylation information from my assembled plant genome using KineticsTool (fasta assembly + Pacbio Sequel dataset).
Now I'd like to perform a downstream analysis to identify and quantify the motifs associated with these DNA modifications. As I mentioned, I'm working on a plant genome, so I'm searching for CG, CHG and CHH (H represents A, T or C) motifs.
I'm aware of MotifMaker and MotifFinder. MotifMaker seems to be specific for prokaryotic genomes. Is MotifMaker albe to perform the motif detection on a plant genome?
I'm not sure of MotifFinder. Has anyone ever used it and can give me some more information?
Are there any other tools for motifs identification specific for plant organisms?