| IMultipleSequenceAligner Interface |
Multiple sequences alignment interface.
Multiple sequence alignment (MSA) is used to align three or
more sequences in preparation for further analysis.
More info on MSA can be found at
http://en.wikipedia.org/wiki/Multiple_sequence_alignment)
Namespace: Bio.Algorithms.Alignment
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe IMultipleSequenceAligner type exposes the following members.
Properties| Name | Description | |
|---|---|---|
 | AlignedSequences |
Gets aligned sequences with equal length by inserting gaps '-' at
appropriate positions so that the alignment score is optimized.
|
| AlignmentScore |
Gets the alignment score of the multiple sequence alignment.
A typical score is the summation of pairwise alignment scores.
|
| 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 |
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.) |
| AlignSimple |
AlignSimple aligns the set of input sequences using the linear gap model (one gap penalty),
and returns the best alignment found.
(Inherited from ISequenceAligner.) |
See Also