| NUCmer Class |
NUCmer is a system for rapidly aligning entire genomes or very large DNA
sequences. It allows alignment of multiple reference sequences to multiple query sequences.
This is commonly used to identify the position and orientation of set of sequence
contigs in relation to finished sequence.
Inheritance HierarchyNamespace: Bio.Algorithms.Alignment
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe NUCmer type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | NUCmer(ISequence) |
Initializes a new instance of the NUCmer class.
|
| NUCmer(ISuffixTree) | Initializes a new instance of the NUCmer class |
Properties| Name | Description | |
|---|---|---|
 | BreakLength |
Gets or sets number of bases to be extended before stopping alignment
|
| ConsensusResolver |
Gets or sets the object that will be used to compute the alignment's consensus.
|
| FixedSeparation |
Gets or sets maximum fixed diagonal difference
|
| GapExtensionCost |
Gets or sets gap extension penalty for use in alignment algorithms.
Not used for alignments using a linear gap penalty.
For alignments using an affine gap, this is the penalty to
extend an existing gap.
This is a negative number, for example GapExtensionCost = -2, not +2.
|
| GapOpenCost |
Gets or sets gap open penalty for use in alignment algorithms.
For alignments using a linear gap penalty, this is the gap penalty.
For alignments using an affine gap, this is the penalty to open a new gap.
This is a negative number, for example GapOpenCost = -8, not +8.
|
| 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
|
| MinimumScore |
Gets or sets minimum output score
|
| ScoreMethod |
Gets or sets the method to use while calculating score of a cluster.
Default is MatchLength.
|
| 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 similarity matrix for use in alignment algorithms.
|
Methods| Name | Description | |
|---|---|---|
| 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.) |
| GetClusters(ListMatchExtension, Boolean) |
get the clusters
|
| GetClusters(ISequence, Boolean, Boolean) |
Gets the clusters
|
| GetDeltaAlignments |
Generates Delta Alignments.
|
| GetHashCode | Serves as the default hash function. (Inherited from Object.) |
| GetType | Gets the Type of the current instance. (Inherited from Object.) |
| MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) |
| ProcessCluster |
Process the cluster
1. Re-map the reference sequence index to original index
2. Create synteny
3. Process synteny
|
| ToString | Returns a string that represents the current object. (Inherited from Object.) |
| ValidateSequenceList |
Validate the list of sequences
|
See Also