I am trying to write a program to screen protein sequences based on their amino acid substitution score.
Initially , tried to do it by simply placing a score of 1 (at relevant substitutions) and 0 where the substitution is deleterious. Is the logic evolutionarily meaningful?
Another thing is , Can i use blosum substitution scores in place of the above mentioned method? I know there is BLAST (ppos available for this). Just want to do in a different way.
Any pointers will be appreciated.