MultiSequenceAlignment.PairWiseScoreFunction Method

MultiSequenceAlignmentPairWiseScoreFunction Method

Calculate pairwise score of a pair of aligned sequences. The score is the sum over all position score given by the similarity matrix. The positions with only indels, e.g. gaps, are discarded. Gaps in the remaining columns are assessed affined score: g + w * e, where g is open penalty, and e is extension 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 static float PairWiseScoreFunction(
	ISequence sequenceA,
	ISequence sequenceB,
	SimilarityMatrix similarityMatrix,
	int gapOpenPenalty,
	int gapExtensionPenalty
)

Public Shared Function PairWiseScoreFunction ( 
	sequenceA As ISequence,
	sequenceB As ISequence,
	similarityMatrix As SimilarityMatrix,
	gapOpenPenalty As Integer,
	gapExtensionPenalty As Integer
) As Single

public:
static float PairWiseScoreFunction(
	ISequence^ sequenceA, 
	ISequence^ sequenceB, 
	SimilarityMatrix^ similarityMatrix, 
	int gapOpenPenalty, 
	int gapExtensionPenalty
)

static member PairWiseScoreFunction : 
        sequenceA : ISequence * 
        sequenceB : ISequence * 
        similarityMatrix : SimilarityMatrix * 
        gapOpenPenalty : int * 
        gapExtensionPenalty : int -> float32

Parameters

sequenceA: Type: BioISequence
aligned sequence
sequenceB: Type: BioISequence
aligned sequence
similarityMatrix: Type: Bio.SimilarityMatricesSimilarityMatrix
similarity matrix
gapOpenPenalty: Type: SystemInt32
negative open gap penalty
gapExtensionPenalty: Type: SystemInt32
negative extension gap penalty

Return Value

Type: Single

[Missing <returns> documentation for "M:Bio.Algorithms.Alignment.MultiSequenceAlignment.PairWiseScoreFunction(Bio.ISequence,Bio.ISequence,Bio.SimilarityMatrices.SimilarityMatrix,System.Int32,System.Int32)"]

Reference

MultiSequenceAlignment Class

Bio.Algorithms.Alignment Namespace