Count of how many single base substitutions result in a change of the amino acid.

silentVsNonsilent.cpp

#include <iostream>
#include <map>

using namespace std;

const static string codon_table[64][2] = {
        {"TTT", "F"}, {"TTC", "F"}, {"TTA", "L"}, {"TTG", "L"}, {"TCT", "S"}, {"TCC", "S"}, {"TCA", "S"}, {"TCG", "S"},
        {"TAT", "Y"}, {"TAC", "Y"}, {"TAA", "X"}, {"TAG", "X"}, {"TGT", "C"}, {"TGC", "C"}, {"TGA", "X"}, {"TGG", "W"},
        {"CTT", "L"}, {"CTC", "L"}, {"CTA", "L"}, {"CTG", "L"}, {"CCT", "P"}, {"CCC", "P"}, {"CCA", "P"}, {"CCG", "P"},
        {"CAT", "H"}, {"CAC", "H"}, {"CAA", "Q"}, {"CAG", "Q"}, {"CGT", "R"}, {"CGC", "R"}, {"CGA", "R"}, {"CGG", "R"},
        {"ATT", "I"}, {"ATC", "I"}, {"ATA", "I"}, {"ATG", "M"}, {"ACT", "T"}, {"ACC", "T"}, {"ACA", "T"}, {"ACG", "T"},
        {"AAT", "N"}, {"AAC", "N"}, {"AAA", "K"}, {"AAG", "K"}, {"AGT", "S"}, {"AGC", "S"}, {"AGA", "R"}, {"AGG", "R"},
        {"GTT", "V"}, {"GTC", "V"}, {"GTA", "V"}, {"GTG", "V"}, {"GCT", "A"}, {"GCC", "A"}, {"GCA", "A"}, {"GCG", "A"},
        {"GAT", "D"}, {"GAC", "D"}, {"GAA", "E"}, {"GAG", "E"}, {"GGT", "G"}, {"GGC", "G"}, {"GGA", "G"}, {"GGG", "G"},
};

const static string bases = "ACGT";

int main(int argc, const char * argv[]){
	int total = 0;
	int silent = 0;
	int nonsilent = 0;

	map<string, string> codons;
	for(int i = 0; i < 64; i++){
		codons[codon_table[i][0]] = codon_table[i][1];
	}

	for(int i = 0; i < 64; i++){
		string triplet = codon_table[i][0];
		string amino_acid = codons[triplet];
		for(int j = 0; j < 3; j++){
			for(int k = 0; k < 4; k++){
				if(bases[k] == triplet[j]){
					continue;
				}
				string temp = triplet;
				temp.at(j) = bases[k];
				string aa = codons[temp];
				total++;
				if(aa == amino_acid){
					silent++;
				}else{
					nonsilent++;
				}
			}
		}

	}

	cout << silent << endl;
	cout << nonsilent << endl;
	cout << total << endl;

	/*
	  result should be
	  silent: 138
	  nonsilent: 438
	  total: 576
	*/
}