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.