This C++ source code implements Smith Waterman Algorithm with affine gap penalties. It requires at least one blank line between the two sequences. Ignores input lines with non-alphabetical characters.
The Smith-Waterman algorithm is used for comparing two sequences, typically biological sequences like DNA, RNA, or proteins. It finds the local similarities between the sequences, identifying regions where they match or align.
Imagine you have two sequences of characters (e.g., A, C, G, T for DNA). The algorithm looks for regions in these sequences where they align well, taking into account matches, mismatches, and gaps.
The algorithm produces an optimal local alignment of the two sequences which shows the regions where they match and any gaps that are introduced to achieve this alignment. The final alignment score reflects the similarity between the aligned regions.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 | #include <iostream> #include <string> #include <cctype> #include <algorithm> #include <locale> using namespace std; const double LARGE_NUMBER = 65536.; const double GAP_OPENING_COST = 10.; const double GAP_EXTENSION_COST = .1; const double NEW_GAP_COST = GAP_OPENING_COST + GAP_EXTENSION_COST; const signed char BLOSUM[][25] = { // the blosum 62 scoring matrix {4, 0, 0, -2, -1, -2, 0, -2, -1, 0, -1, -1, // A -1, -2, 0, -1, -1, -1, 1, 0, 0, 0, -3, 0, -2}, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, {0, 0, 9, -3, -4, -2, -3, -3, -1, 0, -3, -1, // C -1, -3, 0, -3, -3, -3, -1, -1, 0, -1, -2, 0, -2}, {-2, 0, -3, 6, 2, -3, -1, -1, -3, 0, -1, -4, // D -3, 1, 0, -1, 0, -2, 0, -1, 0, -3, -4, 0, -3}, {-1, 0, -4, 2, 5, -3, -2, 0, -3, 0, 1, -3, // E -2, 0, 0, -1, 2, 0, 0, -1, 0, -2, -3, 0, -2}, {-2, 0, -2, -3, -3, 6, -3, -1, 0, 0, -3, 0, // F 0, -3, 0, -4, -3, -3, -2, -2, 0, -1, 1, 0, 3}, {0, 0, -3, -1, -2, -3, 6, -2, -4, 0, -2, -4, // G -3, 0, 0, -2, -2, -2, 0, -2, 0, -3, -2, 0, -3}, {-2, 0, -3, -1, 0, -1, -2, 8, -3, 0, -1, -3, // H -2, 1, 0, -2, 0, 0, -1, -2, 0, -3, -2, 0, 2}, {-1, 0, -1, -3, -3, 0, -4, -3, 4, 0, -3, 2, // I 1, -3, 0, -3, -3, -3, -2, -1, 0, 3, -3, 0, -1}, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, {-1, 0, -3, -1, 1, -3, -2, -1, -3, 0, 5, -2, // K -1, 0, 0, -1, 1, 2, 0, -1, 0, -2, -3, 0, -2}, {-1, 0, -1, -4, -3, 0, -4, -3, 2, 0, -2, 4, // L 2, -3, 0, -3, -2, -2, -2, -1, 0, 1, -2, 0, -1}, {-1, 0, -1, -3, -2, 0, -3, -2, 1, 0, -1, 2, // M 5, -2, 0, -2, 0, -1, -1, -1, 0, 1, -1, 0, -1}, {-2, 0, -3, 1, 0, -3, 0, 1, -3, 0, 0, -3, // N -2, 6, 0, -2, 0, 0, 1, 0, 0, -3, -4, 0, -2}, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, {-1, 0, -3, -1, -1, -4, -2, -2, -3, 0, -1, -3, // P -2, -2, 0, 7, -1, -2, -1, -1, 0, -2, -4, 0, -3}, {-1, 0, -3, 0, 2, -3, -2, 0, -3, 0, 1, -2, // Q 0, 0, 0, -1, 5, 1, 0, -1, 0, -2, -2, 0, -1}, {-1, 0, -3, -2, 0, -3, -2, 0, -3, 0, 2, -2, // R -1, 0, 0, -2, 1, 5, -1, -1, 0, -3, -3, 0, -2}, {1, 0, -1, 0, 0, -2, 0, -1, -2, 0, 0, -2, // S -1, 1, 0, -1, 0, -1, 4, 1, 0, -2, -3, 0, -2}, {0, 0, -1, -1, -1, -2, -2, -2, -1, 0, -1, -1, // T -1, 0, 0, -1, -1, -1, 1, 5, 0, 0, -2, 0, -2}, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, {0, 0, -1, -3, -2, -1, -3, -3, 3, 0, -2, 1, // V 1, -3, 0, -2, -2, -3, -2, 0, 0, 4, -3, 0, -1}, {-3, 0, -2, -4, -3, 1, -2, -2, -3, 0, -3, -2, // W -1, -4, 0, -4, -2, -3, -3, -2, 0, -3, 11, 0, 2}, {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, {-2, 0, -2, -3, -2, 3, -3, 2, -1, 0, -2, -1, // Y -1, -2, 0, -3, -1, -2, -2, -2, 0, -1, 2, 0, 7} }; // trim from start (in place) inline void ltrim(std::string& s) { s.erase(s.begin(), std::find_if(s.begin(), s.end(), [](unsigned char ch) { return !std::isspace(ch); })); } // trim from end (in place) inline void rtrim(std::string& s) { s.erase(std::find_if(s.rbegin(), s.rend(), [](unsigned char ch) { return !std::isspace(ch); }).base(), s.end()); } // trim from both ends (in place) inline void trim(std::string& s) { rtrim(s); ltrim(s); } template<typename T> class Array2D { public: int rows; int cols; T** data; Array2D(int rows, int cols) : rows(rows), cols(cols) { data = new T * [rows]; for (int i = 0; i < rows; ++i) { data[i] = new T[cols](); } } ~Array2D() { for (int i = 0; i < rows; ++i) { delete[] data[i]; } delete[] data; } T** getData() const { return data; } // Overload the subscript operator for convenient access T* operator[](int index) { return data[index]; } // Function to return the number of rows (height) int height() const { return rows; } // Function to return the number of columns (width) int width() const { return cols; } }; void read(string& sequence) { string line; while (getline(cin, line)) { trim(line); if (line.empty()) { return; } for (int i = 0, n = line.length(); i < n; i++) { if (!isalpha(line[i] = toupper(line[i]))) { if (!sequence.empty()) { return; } line = ""; break; } } sequence += line; } } double max(double x, double y) { return x > y ? x : y; } double max(double x, double y, double z) { return x > y ? max(x, z) : max(y, z); } double alignment(string& s1, string& s2) { int n = s1.length() + 1, m = s2.length() + 1, i, j; Array2D<double> r(n, m), t(n, m), s(n, m); //==== // initialization r[0][0] = t[0][0] = s[0][0] = 0; for (i = 1; i < n; i++) { r[i][0] = -LARGE_NUMBER; s[i][0] = t[i][0] = -GAP_OPENING_COST - i * GAP_EXTENSION_COST; } for (j = 1; j < m; j++) { t[0][j] = -LARGE_NUMBER; s[0][j] = r[0][j] = -GAP_OPENING_COST - j * GAP_EXTENSION_COST; } //==== // Smith-Waterman with affine gap costs for (i = 1; i < n; i++) { for (j = 1; j < m; j++) { r[i][j] = max(r[i][j - 1] - GAP_EXTENSION_COST, s[i][j - 1] - NEW_GAP_COST); t[i][j] = max(t[i - 1][j] - GAP_EXTENSION_COST, s[i - 1][j] - NEW_GAP_COST); s[i][j] = max( s[i - 1][j - 1] + BLOSUM[s1[i - 1] - 'A'][s2[j - 1] - 'A'], r[i][j], t[i][j] ); } } //==== // back tracking i = n - 1, j = m - 1; while (i > 0 || j > 0) { if (s[i][j] == r[i][j]) { s1.insert(i, 1, '-'); j--; } else if (s[i][j] == t[i][j]) { s2.insert(j, 1, '-'); i--; } else { i--, j--; } } //==== // final score return s[s.height() - 1][s.width() - 1]; } int main() { string sequence1, sequence2; read(sequence1), read(sequence2); double score = alignment(sequence1, sequence2); cout << sequence1 << "\n\n" << sequence2 << "\n\nScore: " << score << endl; return 0; } |
