| IPairwiseSequenceAligner Interface |
A sequence alignment algorithm that aligns exactly two
sequences. This may diverge from ISequenceAligner at some
point; meanwhile, it's important to maintain the distinction
(e.g., assembly requires a pairwise algorithm).
Namespace: Bio.Algorithms.Alignment
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe IPairwiseSequenceAligner type exposes the following members.
Properties| Name | Description | |
|---|---|---|
 | ConsensusResolver |
Gets or sets the object that will be used to compute the alignment's consensus.
(Inherited from ISequenceAligner.) |
| Description |
Gets the description of the sequence alignment algorithm being
implemented.This is intended to give developer
some information of the alignment algorithm.
(Inherited from ISequenceAligner.) |
| 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.
(Inherited from ISequenceAligner.) |
| GapOpenCost |
Gets or sets value of GapOpenCost
The GapOpenCost is the cost of inserting a gap character into
a sequence.
(Inherited from ISequenceAligner.) |
| Name |
Gets the name of the sequence alignment algorithm being
implemented. This is intended to give developer
some information of the alignment algorithm.
(Inherited from ISequenceAligner.) |
| 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.
(Inherited from ISequenceAligner.) |
Methods| Name | Description | |
|---|---|---|
 | Align(IEnumerableISequence) |
Align aligns the set of input sequences using the affine gap model (gap open and gap extension penalties)
and returns the best alignment found.
(Inherited from ISequenceAligner.) |
| Align(ISequence, ISequence) |
A convenience method - we know there are exactly two inputs.
Align uses the affine gap model, which requires a gap open and a gap extension penalty.
|
| AlignSimple(IEnumerableISequence) |
AlignSimple aligns the set of input sequences using the linear gap model (one gap penalty),
and returns the best alignment found.
(Inherited from ISequenceAligner.) |
| AlignSimple(ISequence, ISequence) |
A convenience method - we know there are exactly two inputs.
AlignSimple uses a single gap penalty.
|
See Also