| MUMmer Class |
MUMmer is a system for rapidly aligning entire genomes or very large protein
sequences. It is a pair wise sequence algorithm. The algorithm assumes the
sequences are closely related, and using this assumption can quickly compare
sequences that are millions of nucleotides in length. The algorithm is
designed to perform high resolution comparison of genome-length sequences.
Inheritance HierarchyNamespace: Bio.Algorithms.MUMmer
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe MUMmer type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | MUMmer(ISequence) |
Initializes a new instance of the MUMmer class with specified reference sequence.
|
| MUMmer(ISuffixTree) |
Initializes a new instance of the MUMmer class with the specified suffix tree.
This enables to use custom suffix tree.
|
Properties| Name | Description | |
|---|---|---|
 | Description |
Gets or sets the description of the MUMmer.
|
| LengthOfMUM |
Gets or sets the length of MUM.
|
| Name |
Gets the name of the MUMmer.
|
| NoAmbiguity |
Gets or sets a value indicating whether only basic symbols should be matched.
Thus the matches will not contains any ambiguous symbols.
|
| ReferenceSequence |
Gets the referenceSequence.
|
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.) |
| GetHashCode | Serves as the default hash function. (Inherited from Object.) |
| GetMatches |
Gets the maximum matches - MaxMatch.
This method does not considers uniqueness.
|
| GetMatchesUniqueInReference |
Gets the maximum unique matches in reference sequence.
|
| GetType | Gets the Type of the current instance. (Inherited from Object.) |
| 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