I have a question about sequence alignment (i known that it isn't the subject of this forum, but i'll be very glad for any help). From a alignment, i intend to extract the consensus sequence differently. I keep only the aa that are really conserved (and probably structurally important). The others, I substituted by the aa G (for example: GGGDGGGRKGGGHEGG, where the aa D,R,K,H and E are very conserved in the protein's alignment). My aim is to modeler the consensus folding to the classes of protein in my study, emphasizing only the functionally important aa. I don't known if I really have a useful structural information or not. If not, i'll be very glad for any advice.
Thanks, Cassiano Carromeu.