GENOME SEQUENCE ALIGNMENT APPARATUS AND METHOD
First Claim
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1. A method for aligning a read sequence to a reference sequence, the method comprising:
- searching a reference sequence for a candidate position matched with a fragment, the fragment being a portion of a read sequence; and
mapping the read sequence to the reference sequence on the candidate position;
wherein the searching and the mapping are implemented at least in part by a hardware processor.
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Abstract
Provided are a sequence alignment apparatus and method for searching a reference sequence for a candidate position matching with a fragment that is a portion of a read sequence, and mapping the reference sequence and the read sequence to each other based on the candidate position. Accordingly, it is possible to form an alignment permitting all variations and errors that may exist in a read sequence, to search the entire area of a read sequence for variations and errors, and to form an alignment with less computation without permitting backtracking, unlike existing sequence alignment technology.
63 Citations
22 Claims
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1. A method for aligning a read sequence to a reference sequence, the method comprising:
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searching a reference sequence for a candidate position matched with a fragment, the fragment being a portion of a read sequence; and mapping the read sequence to the reference sequence on the candidate position; wherein the searching and the mapping are implemented at least in part by a hardware processor. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
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13. A computer program product comprising a non-transitory computer-readable medium and computer instructions configured to enable a hardware processor to implement:
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a position selector configured to search a reference sequence for a candidate position matched with a fragment, the fragment being a portion of a read sequence; a mapper configured to map the read sequence to the reference sequence on the candidate position; and an aligner configured to align the read sequence with the candidate position when the reference sequence and the read sequence match with each other at the candidate position.
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14. An apparatus intended for use in aligning a read sequence to a reference sequence, the apparatus comprising:
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a position selector configured to search a reference sequence for a candidate position matched with a fragment, the fragment being a portion of a read sequence; a mapper configured to map the read sequence to the reference sequence on the candidate position; and an aligner configured to align the read sequence with the candidate position when the reference sequence and the read sequence match with each other at the candidate position wherein at least one of the position selector, the mapper, and the aligner is implemented using a hardware processor. - View Dependent Claims (15, 16, 17, 18, 19, 20, 21, 22)
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Specification