Optimal Pair-wise Sequence Alignment
It implements Smith-Waterman with affine gap penalties. It requires at least one blank line between the two sequences. Ignores input lines with non-alphabetical characters
This program is provided as is with no warranty. The author is not responsible for any damage caused either directly or indirectly by using this program. Anybody is free to do whatever he/she wants with this program as long as this header section is preserved.
Created on 2005-02-01 by Roger Zhang ([email protected])
Last compiled under Linux with gcc-3
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 | /******************************************************* * MYCPLUS Sample Code - https://www.mycplus.com * * * * This code is made available as a service to our * * visitors and is provided strictly for the * * purpose of illustration. * * * * Please direct all inquiries to saqib at mycplus.com * *******************************************************/ //==== // opsa.cpp // - Optimal Pair-wise Sequence Alignment // - implements Smith-Waterman with affine gap penalties // - requires at least one blank line between the two sequences // - ignores input lines with non-alphabetical characters // Notes // - This program is provided as is with no warranty. // - The author is not responsible for any damage caused // either directly or indirectly by using this program. // - Anybody is free to do whatever he/she wants with this // program as long as this header section is preserved. // Created on 2005-02-01 by // - Roger Zhang ([email protected]) // Modifications // - Roger Zhang on 2005-02-18 // - Hard coded the blosum matrix to remove external dependency // - // Last compiled under Linux with gcc-3 //==== #include <iostream> #include <string> #include <cctype> #include "Array2D.hpp" // see http://cs.smu.ca/~r_zhang/a2h #include "strUtil.hpp" // see http://cs.smu.ca/~r_zhang/suh using namespace std; using namespace RZ; 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} }; 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; } |
