Example Program
Needleman-Wunsch Algorithm
Needleman-Wunsch alignment code example
File "graph_align_nw.cpp"
This code example illustrates a graph-based Needleman-Wunsch alignment
1#include <seqan/graph_align.h>
2#include <iostream>
3
4using namespace seqan;
5
6int main() {
7    typedef String<char> TString;
8    typedef StringSet<TString, Dependent<> > TStringSet;
9    typedef Graph<Alignment<TStringSet, void> > TGraph;
Alignments are carried out on a StringSet that holds the sequences
10    TStringSet str;
11    TString str0("Myannealing");appendValue(str, str0);
12    TString str1("annual"); appendValue(str, str1);
Configuration of alignment algorithm: Scoring (Match = 0, Mismatch = -1, Gap = -1)
13    Score<int> score_type = Score<int>(0,-1,-1,0);
Out-parameter: An alignment graph
14    TGraph g(str);
Global alignment with Needleman-Wunsch
15    int score = globalAlignment(g, score_type, NeedlemanWunsch() );
Console output
16    std::cout << "Scoring schema: Match=0, Mismatch=-1, Gap=-1" << std::endl;
17    std::cout << g << std::endl;
18    std::cout << "Score: " << score << std::endl;
The initialization of the matrix and the traceback start can also be controlled. Configuration: AlignConfig<TTop, TLeft, TRight, TBottom>. If TTop, TLeft, TRight, or TBottom is true the corresponding row / column is initialized with 0's or searched for the maximum, respectively.
19    AlignConfig<true,false,false,true> ac;
Global alignment with Needleman-Wunsch and special initialization
20    int score2 = globalAlignment(stringSet(g), score_type, ac, NeedlemanWunsch() );
Console output
21    std::cout << "Score with ends free-space alignment: " << score2 << std::endl;
22    return 0;
23}
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