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#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/stream.h> // for I/O
#include <seqan/align.h>
#include <seqan/score.h>
using namespace seqan;
int main()
{
StringSet<DnaString> stringSet;
appendValue(stringSet, "ACGTGGATCGGTGACTTACGGACTG");
appendValue(stringSet, "ACGTGTTGAGTGATTACGGACTG");
Align<DnaString> align(stringSet); // Initialize the Align object using a StringSet.
Score<int> scoreScheme(5, -6, -2, -11); // Initialize Score object with affine gap costs.
int score = globalAlignment(align, scoreScheme); // Computes a global alignment usign the defined scoring scheme.
std::cout << "Score = " << score << std::endl;
std::cout << "Alignment:" << std::endl;
std::cout << align << std::endl;
return 0;
}
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