Title:
METHODS, COMPUTER-ACCESSIBLE MEDIUM, AND SYSTEMS FOR SCORE-DRIVEN WHOLE-GENOME SHOTGUN SEQUENCE ASSEMBLE
Document Type and Number:
WIPO Patent Application WO/2010/075570
Kind Code:
A3
Abstract:
Exemplary embodiments of the present disclosure relate generally to methods, computer-accessible medium and systems for assembling haplotype and/or genotype sequences of at least one genome, which can be based upon, e.g., consistent layouts of short sequence reads and long-range genome related data. For example, a processing arrangement can be configured to perform a procedure including, e.g., obtaining randomly located short sequence reads, using at least one score function in combination with constraints based on, e.g., the long range data, generating a layout of randomly located short sequence reads such that the layout is globally optimal with respect to the score function, obtained through searching coupled with score and constraint dependent pruning to determine the globally optimal layout substantially satisfying the constraints, generating a whole and/or a part of a genome wide haplotype sequence and/or genotype sequence, and converting a globally optimal layout into one or more consensus sequences.
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Inventors:
MISHRA BHUBANESWAR (US)
NARZISI GIUSEPPE (US)
NARZISI GIUSEPPE (US)
Application Number:
PCT/US2009/069509
Publication Date:
October 28, 2010
Filing Date:
December 23, 2009
Export Citation:
Assignee:
UNIV NEW YORK (US)
MISHRA BHUBANESWAR (US)
NARZISI GIUSEPPE (US)
MISHRA BHUBANESWAR (US)
NARZISI GIUSEPPE (US)
International Classes:
G16B30/20; C12Q1/68; G16B30/10
Other References:
ADAM M PHILLIPPY ET AL.: "Genome assembly forensics : finding the elusive mis-assembly", GENOME BIOLOGY, vol. 9, no. IS SUE, March 2008 (2008-03-01)
J. D. KECECIOGLU ET AL.: "Combinatorial Algorithms for DNA Sequence Assembly", ALGORITHMICA, vol. 13, no. 1-2, 1995, pages 7 - 51
SCOTT C.-H. PEGG ET AL.: "Shotgun: getting more from sequenc e similarity searches", BIOINFORMATICS, vol. 15, no. 9, September 1999 (1999-09-01), pages 729 - 740
D. Y. LIN ET AL.: "Likelihood-Based Inference on Haplotype Effects in Ge netic Association Studies", JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, vol. 101, no. 473, March 2006 (2006-03-01), pages 89 - 104
MUKUND SUNDARARAJAN ET AL.: "Chaining Algorithms for Alignment of Draft Seque nce", ALGORITHMS IN BIOINFORMATICS, vol. 3240/200, September 2004 (2004-09-01), pages 3 26 - 337
J. D. KECECIOGLU ET AL.: "Combinatorial Algorithms for DNA Sequence Assembly", ALGORITHMICA, vol. 13, no. 1-2, 1995, pages 7 - 51
SCOTT C.-H. PEGG ET AL.: "Shotgun: getting more from sequenc e similarity searches", BIOINFORMATICS, vol. 15, no. 9, September 1999 (1999-09-01), pages 729 - 740
D. Y. LIN ET AL.: "Likelihood-Based Inference on Haplotype Effects in Ge netic Association Studies", JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, vol. 101, no. 473, March 2006 (2006-03-01), pages 89 - 104
MUKUND SUNDARARAJAN ET AL.: "Chaining Algorithms for Alignment of Draft Seque nce", ALGORITHMS IN BIOINFORMATICS, vol. 3240/200, September 2004 (2004-09-01), pages 3 26 - 337
Attorney, Agent or Firm:
ACKERMAN, Paul et al. (250 Park AvenueNew York, NY, US)
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