Hello, I am looking at insertions/deletions occurring at various places in my protein and also I want to map the active site residues. I have performed Multiple sequence alignment as well as multiple structure based alignment for my protein of study. I have obtained different alignment patterns in sequence and structural alignment. My question is which alignment pattern should I consider? Whether to go for insertions/deletions as per the sequence alignment or based on structure. And why should I prefer it? Which is more reliable? I would like to study the evolutionary pattern of my protein.
Please help me out,,,, Thanks, -Suda
