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US 2003/0224384 A1Published application
Divide and conquer system and method of DNA sequence assembly
OwnerKhalid Sayood, Hasan H. Otuinventors
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Abstract
The present invention provides a new algorithm for assembling fragments from a long DNA sequence. The algorithm of the invention solves simultaneously fragment assembly-related problems such as the fragment orientation, overlap and layout phases. This is achieved by clustering fragments with respect to their Average Mutual Information (AMI) profiles using the k-means algorithm.
Claims20
A method of assembling subsequences of a DNA sequence comprising the steps of:
- assigning a numerical characterization to each subsequence, each numerical characterization comprising a set of numbers;
- clustering the sets;
- and
- aligning the sets to form a consensus sequence for each cluster.
1 more element
A system of assembling subsequences of a DNA sequence comprising:
- a database of the subsequences to be assembled;
- and
- a processor accessing the subsequences in the database and having software for:
- assigning a numerical characterization to each subsequence, each numerical characterization comprising a set of numbers;
- clustering the sets;
- and
- aligning the sets to form a consensus sequence for each cluster.
4 more elements
A system of assembling subsequences of a DNA sequence comprising:
- a database of the subsequences to be assembled;
- and
- a processor accessing the subsequences in the database and having software for:
- assigning a numerical characterization to each subsequence, each numerical characterization comprising a set of numbers;
- defining a vector for each subsequence, each vector having coordinates corresponding to the numerical characterizations of one subsequence;
- clustering the vectors;
- and
- aligning the vectors, wherein said aligning comprises comparing the vectors in each cluster and aligning the subsequences of corresponding compared vectors to form a consensus sequence for each cluster.
5 more elements
Dependencies are inferred from the claim text.