Data processing system and methods
First Claim
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1. A method of identifying a nucleotide base in a nucleic acid sequence, said method comprising:
- determining the intensity of each differently colored signal present at a particular feature on an array at a particular time, wherein each differently colored signal corresponds to a different nucleotide base;
repeating said determining step for a plurality of features on an array at said particular time;
refining the signal intensity for said plurality of features then repeating said determining step for said plurality of features; and
selecting for each feature of said plurality of features the refined signal having the highest intensity, wherein said signal having the highest intensity at a particular feature corresponds the identity of the nucleotide base present at said particular feature.
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Abstract
Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.
51 Citations
22 Claims
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1. A method of identifying a nucleotide base in a nucleic acid sequence, said method comprising:
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determining the intensity of each differently colored signal present at a particular feature on an array at a particular time, wherein each differently colored signal corresponds to a different nucleotide base; repeating said determining step for a plurality of features on an array at said particular time; refining the signal intensity for said plurality of features then repeating said determining step for said plurality of features; and selecting for each feature of said plurality of features the refined signal having the highest intensity, wherein said signal having the highest intensity at a particular feature corresponds the identity of the nucleotide base present at said particular feature.
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2. A method of selecting a signal from a cluster of signals in an image, comprising:
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discarding any signals that do not appear within a cluster of signals, the cluster of signals having a defined cluster radius; and selecting the signal with the highest intensity of signals within a cluster, wherein the selecting comprises a chastity determination comprising; (a) generating a list of identified spots and intensities for each template cycle, (b) providing a preliminary base call for each spot, (c) determining the chastity of each base call, (d) identifying spots with two or more chastity failures, (e) eliminating spots having chastity values lower than a threshold value, (f) determining the sample diversity and/or the probability that clusters will match base calls by chance, and (g) analyzing spots in iteration from highest to lowest chastity over template cycles. - View Dependent Claims (3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22)
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Specification