public void SmithWatermanProteinSeqAffineGap()
{
IPairwiseSequenceAligner sw = new SmithWatermanAligner
{
SimilarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62),
GapOpenCost = -8,
GapExtensionCost = -1,
};
ISequence sequence1 = new Sequence(Alphabets.Protein, "HEAGAWGHEE");
ISequence sequence2 = new Sequence(Alphabets.Protein, "PAWHEAE");
IList <IPairwiseSequenceAlignment> result = sw.Align(sequence1, sequence2);
AlignmentHelpers.LogResult(sw, result);
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.Protein, "AWGHE"),
SecondSequence = new Sequence(Alphabets.Protein, "AW-HE"),
Consensus = new Sequence(Alphabets.AmbiguousProtein, "AWGHE"),
Score = 20,
FirstOffset = 0,
SecondOffset = 3
};
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
}
public void NeedlemanWunschProteinSeqAffineGap()
{
IPairwiseSequenceAligner nw = new NeedlemanWunschAligner
{
SimilarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62),
GapOpenCost = -8,
GapExtensionCost = -1
};
ISequence sequence1 = new Sequence(Alphabets.Protein, "HEAGAWGHEE");
ISequence sequence2 = new Sequence(Alphabets.Protein, "PAWHEAE");
IList <IPairwiseSequenceAlignment> result = nw.Align(sequence1, sequence2);
AlignmentHelpers.LogResult(nw, result);
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.Protein, "HEAGAWGHE-E"),
SecondSequence = new Sequence(Alphabets.Protein, "P---AW-HEAE"),
Consensus = new Sequence(AmbiguousProteinAlphabet.Instance, "XEAGAWGHEAE"),
Score = 5,
FirstOffset = 0,
SecondOffset = 0
});
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
}
public void NeedlemanWunschDnaSeqSimpleGap()
{
IPairwiseSequenceAligner nw = new NeedlemanWunschAligner
{
SimilarityMatrix = new DiagonalSimilarityMatrix(2, -1),
GapOpenCost = -2
};
ISequence sequence1 = new Sequence(Alphabets.DNA, "GAATTCAGTTA");
ISequence sequence2 = new Sequence(Alphabets.DNA, "GGATCGA");
IList <IPairwiseSequenceAlignment> result = nw.AlignSimple(sequence1, sequence2);
AlignmentHelpers.LogResult(nw, result);
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "GAATTCAGTTA"),
SecondSequence = new Sequence(Alphabets.DNA, "GGAT-C-G--A"),
Consensus = new Sequence(AmbiguousDnaAlphabet.Instance, "GRATTCAGTTA"),
Score = 3,
FirstOffset = 0,
SecondOffset = 0
});
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
}
public void SmithWatermanAlignerMultipleAlignments2()
{
IPairwiseSequenceAligner sw = new SmithWatermanAligner
{
SimilarityMatrix = new DiagonalSimilarityMatrix(5, -4),
GapOpenCost = -5
};
ISequence sequence1 = new Sequence(Alphabets.DNA, "AAAAGGGGGGCCCC");
ISequence sequence2 = new Sequence(Alphabets.DNA, "AAAATTTTTTTCCCC");
IList <IPairwiseSequenceAlignment> result = sw.AlignSimple(sequence1, sequence2);
AlignmentHelpers.LogResult(sw, result);
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
// First alignment
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment(sequence1, sequence2);
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "AAAA"),
SecondSequence = new Sequence(Alphabets.DNA, "AAAA"),
Consensus = new Sequence(Alphabets.DNA, "AAAA"),
Score = 20,
FirstOffset = 0,
SecondOffset = 0
});
// Second alignment
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "CCCC"),
SecondSequence = new Sequence(Alphabets.DNA, "CCCC"),
Consensus = new Sequence(Alphabets.DNA, "CCCC"),
Score = 20,
FirstOffset = 1,
SecondOffset = 0
});
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
}