I am new to R, and I would like some tips on motif detection in a protein multiple sequence alignment. I would like to extract the motifs using only some parts of the alignment (ex. aa 23-58, 123-567 etc).
I have already created a multiple sequence alignment of orthologues of this protein using MAFFT (browser version).
Some recommend to use MEME to create pssm.
So I would like some recommendations for packages, tools and any strategic tips for my research.
I will truly appreciate any help.
Thank you in advance.