Methods for accurate sequence data and modified base position determination
First Claim
1. A method of determining the sequence of a nucleic acid sample comprising:
- a. generating a nucleic acid molecule from a linear pair-locked molecule to obtain sequence data from the linear pair-locked molecule,the linear pair-locked molecule and the nucleic acid molecule each comprising at least two insert-sample units each comprising a nucleic acid insert and the nucleic acid sample, wherein the nucleic acid insert has a known sequence, and the nucleic acid insert is immediately upstream or downstream to the nucleic acid sample,and the sequence data comprising sequence data of at least two insert-sample units, wherein the sequence data of at least two insert-sample units each comprise a repeat of the sequence of the nucleic acid sample;
b. calculating scores of the sequences of at least two inserts of the sequence data of step (a) by comparing the sequences to the known sequence of the insert;
c. accepting or rejecting at least two of the repeats of the sequence of the nucleic acid sample of the sequence data of step (a) according to the scores of one or both of the sequences of the inserts;
d. compiling an accepted sequence set comprising at least one repeat of the sequence of the nucleic acid sample accepted in step (c); and
e. determining the sequence of the nucleic acid sample using the accepted sequence set.
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Accused Products
Abstract
Disclosed herein are methods of determining the sequence and/or positions of modified bases in a nucleic acid sample present in a circular molecule with a nucleic acid insert of known sequence comprising obtaining sequence data of at least two insert-sample units. In some embodiments, the methods comprise obtaining sequence data using circular pair-locked molecules. In some embodiments, the methods comprise calculating scores of sequences of the nucleic acid inserts by comparing the sequences to the known sequence of the nucleic acid insert, and accepting or rejecting repeats of the sequence of the nucleic acid sample according to the scores of one or both of the sequences of the inserts immediately upstream or downstream of the repeats of the sequence of the nucleic acid sample.
25 Citations
34 Claims
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1. A method of determining the sequence of a nucleic acid sample comprising:
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a. generating a nucleic acid molecule from a linear pair-locked molecule to obtain sequence data from the linear pair-locked molecule, the linear pair-locked molecule and the nucleic acid molecule each comprising at least two insert-sample units each comprising a nucleic acid insert and the nucleic acid sample, wherein the nucleic acid insert has a known sequence, and the nucleic acid insert is immediately upstream or downstream to the nucleic acid sample, and the sequence data comprising sequence data of at least two insert-sample units, wherein the sequence data of at least two insert-sample units each comprise a repeat of the sequence of the nucleic acid sample; b. calculating scores of the sequences of at least two inserts of the sequence data of step (a) by comparing the sequences to the known sequence of the insert; c. accepting or rejecting at least two of the repeats of the sequence of the nucleic acid sample of the sequence data of step (a) according to the scores of one or both of the sequences of the inserts; d. compiling an accepted sequence set comprising at least one repeat of the sequence of the nucleic acid sample accepted in step (c); and e. determining the sequence of the nucleic acid sample using the accepted sequence set. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34)
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Specification