Method and system for comparative genomics
AssigneeInternational Business Machines Corporation
InventorsGad M. Landau, Laxmi Priya Parida, Oren Weimann
Life of this patent
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Abstract
A method and system for representing a similarity between at least two genomes that includes detecting gene clusters which are common to the at least two genomes and representing the common gene clusters in a PQ tree. The PQ tree includes a first internal node (P node), that allows permutation of the children thereof, and a second internal node (Q node), that maintains unidirectional order of the children thereof.
Claims14
A method of representing a similarity between at least two genomes, said method comprising:
- detecting gene clusters which are common to said at least two genomes:
- on a processor of a computer, representing said common gene clusters in a PQ tree, wherein said PQ tree comprises:
- a first internal node (P node) that allows a permutation of children thereof;
- and
- a second internal node (Q node) that maintains a unidirectional order of the children thereof;
- and
- filtering said gene clusters,
- wherein said PQ tree comprises a minimal consensus PQ tree.
The method of claim wherein, given k permutations on an b1 alphabet Σ, representing k occurrences of a pattern, a maximal notation is obtained by using a ‘-’ between said two genes to denote that these groups appear as immediate neighbors in all the k permutations, and using a ‘,’ otherwise.
A system for representing a similarity between at least two genomes, said system comprising:
- a detector that detects gene clusters which are common to said at least two genomes;
- a processor that represents said common gene clusters in a PQ tree, wherein said PQ tree comprises:
- a first internal node (P node) that allows a permutation of children thereof;
- and
- a second internal node (Q node) that maintains a unidirectional order of the children thereof;
- and
- a filter that filters said gene clusters,
- wherein said PQ tree comprises a minimal consensus PQ tree.
A non-transitory computer-readable storage medium encoded with a computer program embodied in a computer readable medium executable by a digital processing unit, said program comprising:
- instructions for detecting gene clusters which are common to at least two genomes;
- instructions for representing said common gene clusters in a PQ tree, wherein said PQ tree comprises:
- a first internal node (P node) that allows a permutation of children thereof;
- and
- a second internal node (Q node) that maintains a unidirectional order of the children thereof;
- and
- instructions for filtering said gene clusters;
- wherein said PQ tree comprises a minimal consensus PQ tree.
Dependencies are inferred from the claim text.