PairwiseSequenceAligner.Align Method (SimilarityMatrix, Int32, Int32, ISequence, ISequence)

PairwiseSequenceAlignerAlign Method (SimilarityMatrix, Int32, Int32, ISequence, ISequence)

Pairwise alignment of two sequences using an affine gap penalty. The various algorithms in derived classes (NeedlemanWunsch, SmithWaterman, and PairwiseOverlap) all use this general engine for alignment with an affine 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> Align(
	SimilarityMatrix localSimilarityMatrix,
	int gapOpenPenalty,
	int gapExtensionPenalty,
	ISequence inputA,
	ISequence inputB
)

Public Function Align ( 
	localSimilarityMatrix As SimilarityMatrix,
	gapOpenPenalty As Integer,
	gapExtensionPenalty As Integer,
	inputA As ISequence,
	inputB As ISequence
) As IList(Of IPairwiseSequenceAlignment)

public:
IList<IPairwiseSequenceAlignment^>^ Align(
	SimilarityMatrix^ localSimilarityMatrix, 
	int gapOpenPenalty, 
	int gapExtensionPenalty, 
	ISequence^ inputA, 
	ISequence^ inputB
)

member Align : 
        localSimilarityMatrix : SimilarityMatrix * 
        gapOpenPenalty : int * 
        gapExtensionPenalty : int * 
        inputA : ISequence * 
        inputB : ISequence -> IList<IPairwiseSequenceAlignment>

Parameters

localSimilarityMatrix: Type: Bio.SimilarityMatricesSimilarityMatrix
Scoring matrix.
gapOpenPenalty: Type: SystemInt32
Gap open penalty (by convention, use a negative number for this.).
gapExtensionPenalty: Type: SystemInt32
Gap extension 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

PairwiseSequenceAligner Class

Align Overload

Bio.Algorithms.Alignment Namespace