DynamicProgrammingPairwiseAligner.AlignSimple Method (SimilarityMatrix, Int32, ISequence, ISequence)

DynamicProgrammingPairwiseAlignerAlignSimple Method (SimilarityMatrix, Int32, ISequence, ISequence)

Pairwise alignment of two sequences using a linear gap penalty. The various algorithms in derived classes (NeedlemanWunsch, SmithWaterman, and PairwiseOverlap) all use this general engine for alignment with a linear gap penalty.

Namespace: Bio.Algorithms.Alignment
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)

Syntax

C++

Copy

public IList<IPairwiseSequenceAlignment> AlignSimple(
	SimilarityMatrix localSimilarityMatrix,
	int gapPenalty,
	ISequence inputA,
	ISequence inputB
)

Public Function AlignSimple ( 
	localSimilarityMatrix As SimilarityMatrix,
	gapPenalty As Integer,
	inputA As ISequence,
	inputB As ISequence
) As IList(Of IPairwiseSequenceAlignment)

public:
IList<IPairwiseSequenceAlignment^>^ AlignSimple(
	SimilarityMatrix^ localSimilarityMatrix, 
	int gapPenalty, 
	ISequence^ inputA, 
	ISequence^ inputB
)

member AlignSimple : 
        localSimilarityMatrix : SimilarityMatrix * 
        gapPenalty : int * 
        inputA : ISequence * 
        inputB : ISequence -> IList<IPairwiseSequenceAlignment>

Parameters

localSimilarityMatrix: Type: Bio.SimilarityMatricesSimilarityMatrix
Scoring matrix.
gapPenalty: Type: SystemInt32
Gap penalty (by convention, use a negative number for this.).
inputA: Type: BioISequence
First input sequence.
inputB: Type: BioISequence
Second input sequence.

Return Value

Type: IListIPairwiseSequenceAlignment
A list of sequence alignments.

Reference

DynamicProgrammingPairwiseAligner Class

AlignSimple Overload

Bio.Algorithms.Alignment Namespace