| NucmerPairwiseAligner Class |
Class which uses nucmer to perform an alignment.
Inheritance HierarchyNamespace: Bio.Algorithms.Alignment
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe NucmerPairwiseAligner type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | NucmerPairwiseAligner | Initializes a new instance of the NucmerPairwiseAligner class |
Properties| Name | Description | |
|---|---|---|
 | BreakLength |
Gets or sets number of bases to be extended before stopping alignment.
|
| ConsensusResolver |
Gets or sets the consensus resolver attached with this aligner.
|
| Description |
Gets or Sets the description of the algorithm.
|
| FixedSeparation |
Gets or sets maximum fixed diagonal difference.
|
| ForwardOnly |
Align only the forward strands of each sequence.
|
| GapExtensionCost |
Gets or sets the Gap Extension Cost.
|
| GapOpenCost |
Gets or sets the Gap Open Cost.
|
 | IsAlign |
Gets or sets a value indicating whether to run Align or AlignSimple.
|
| LengthOfMUM |
Gets or sets minimum length of Match that can be considered as MUM.
|
| MaximumSeparation |
Gets or sets maximum separation between the adjacent matches in clusters.
|
| MaxMatch |
Use all anchor matches regardless of their uniqueness.
|
| MinimumScore |
Gets or sets minimum output score.
|
| Name |
Gets or Sets the name of the algorithm.
|
| ReverseOnly |
Align only the reverse strands of each sequence.
|
| SeparationFactor |
Gets or sets separation factor. Fraction equal to
(diagonal difference / match separation) where higher values
increase the insertion or deletion (indel) tolerance.
|
| SimilarityMatrix |
Gets or sets the similarity matrix associated with this aligner.
|
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.
|
| Align(ISequence, 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.
|
| Align(IEnumerableISequence, 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.
|
| AlignSimple |
AlignSimple aligns the set of input sequences using the linear gap model (one gap penalty),
and returns the best alignment found.
|
 | CalculateScore |
Calculate the score of alignment.
|
 | ConcatSequence |
Concat all the sequences into one sequence with special character.
|
| Equals | Determines whether the specified object is equal to the current object. (Inherited from Object.) |
| Finalize | Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection. (Inherited from Object.) |
| GetHashCode | Serves as the default hash function. (Inherited from Object.) |
| GetType | Gets the Type of the current instance. (Inherited from Object.) |
| MakeConsensus |
Analyze the given sequences and store a consensus into its Consensus property.
|
| MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) |
| ToString | Returns a string that represents the current object. (Inherited from Object.) |
See Also