ISequenceAligner Interface

A sequence aligner is an algorithm which takes N sequences as input and produces an alignment of the sequences as output.

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

Syntax

public interface ISequenceAligner

Public Interface ISequenceAligner

public interface class ISequenceAligner

type ISequenceAligner =  interface end

The ISequenceAligner type exposes the following members.

Properties

	Name	Description
	ConsensusResolver	Gets or sets the object that will be used to compute the alignment's consensus.
	Description	Gets the description of the sequence alignment algorithm being implemented.This is intended to give developer some information of the alignment algorithm.
	GapExtensionCost	Gets or sets value of GapExtensionCost The GapExtensionCost is the cost of extending an already existing gap. This is used for the affine gap model, not used for the linear gap model.
	GapOpenCost	Gets or sets value of GapOpenCost The GapOpenCost is the cost of inserting a gap character into a sequence.
	Name	Gets the name of the sequence alignment algorithm being implemented. This is intended to give developer some information of the alignment algorithm.
	SimilarityMatrix	Gets or sets value of similarity matrix The similarity matrix determines the score for any possible pair of symbols that are encountered at a common location across the sequences being aligned.

Methods

	Name	Description
	Align	Align aligns the set of input sequences using the affine gap model (gap open and gap extension penalties) and returns the best alignment found.
	AlignSimple	AlignSimple aligns the set of input sequences using the linear gap model (one gap penalty), and returns the best alignment found.