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#include <seqan/align.h>
#include <seqan/stream.h>
#include <seqan/score.h>
#include <seqan/seeds.h>
#include <seqan/sequence.h>
using namespace seqan;
int main()
{
// The horizontal and vertical sequence (subject and query sequences).
CharString seqH = "The quick BROWN fox jumped again!";
CharString seqV = "thick BROWN boxes of brownies!";
// Create the seed sequence.
Seed<Simple> seed(11, 7, 14, 10);
// Perform match extension.
Score<int, Simple> scoringScheme(1, -1, -2, -2);
extendSeed(seed, seqH, seqV, EXTEND_BOTH, scoringScheme, 3,
GappedXDrop());
// Perform a banded alignment.
Align<CharString> align;
resize(rows(align), 2);
assignSource(row(align, 0), infix(seqH, beginPositionH(seed),
endPositionH(seed)));
assignSource(row(align, 1), infix(seqV, beginPositionV(seed),
endPositionV(seed)));
globalAlignment(align, scoringScheme);
std::cout << "Resulting alignment\n" << align << "\n";
return 0;
}
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