Patent US5795716A successfully refreshed from Google Patents.
US5795716A
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Computer-aided visualization and analysis system for sequence evaluation
Assignee: Affymetrix Inc
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Filing: 1994-10-21
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Granted: 1998-08-18
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Expires: 2014-10-21
Abstract
Abstract A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments are improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.
Inventors
- 👤 Mark S. Chee
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-11-09 21:36
CPC Classifications
G; G16; G16B; G16B30/00; B; B01; B01J; B01J19/00; B01J19/0046; B82; B82Y; B82Y30/00; C; C12; C12Q; C12Q1/00; C12Q1/68; C12Q1/6813; C12Q1/6827; C12Q1/6869; C12Q1/6874; G16B25/00; G16B25/20; G16B30/20; B01J2219/00; B01J2219/00274; B01J2219/00277; B01J2219/00351; B01J2219/00427; B01J2219/00432; B01J2219/00497; B01J2219/00527; B01J2219/00529; B01J2219/00583; B01J2219/00603; B01J2219/00605; B01J2219/00608; B01J2219/0061; B01J2219/00612; B01J2219/00614; B01J2219/00617; B01J2219/00623; B01J2219/00626; B01J2219/00659; B01J2219/0068; B01J2219/00686; B01J2219/00689; B01J2219/00695; B01J2219/00709; B01J2219/00711; B01J2219/00718; B01J2219/0072; B01J2219/00722; C40; C40B; C40B40/00; C40B40/04; C40B40/06; C40B60/00; C40B60/14; G01; G01N; G01N15/00; G01N15/10; G01N15/14; G01N15/1429; G01N15/1433
Claims Analysis
Total Claims: 18
Claim 1
Independent Claim
124 words
A computer program product that identifies an unknown base in a sample nucleic acid sequence, comprising: computer code that receives a plurality of signals corresponding to probe intensities for a plurality of nucleic acid probes, each probe intensity indicating an extent of hybridization of a nucleic acid probe with at least one nucleic acid sequence including said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that performs a comparison of said plurality of probe intensities to each other; computer code that generates a base call identifying said unknown base according to results of said comparison and said sequences of said nucleic acid probes; and a computer readable medium that stores said computer codes.
Claim 2
Dependent Claim
124 words
A computer program product that identifies an unknown base in a sample nucleic acid sequence, comprising: computer code that receives a plurality of signals corresponding to probe intensities for a plurality of nucleic acid probes, each probe intensity indicating an extent of hybridization of a nucleic acid probe with at least one nucleic acid sequence including said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that performs a comparison of said plurality of probe intensities to each other; computer code that generates a base call identifying said unknown base according to results of said comparison and said sequences of said nucleic acid probes; and a computer readable medium that stores said computer codes.
Claim 3
Dependent Claim
128 words
A computer program product that identifies an unknown base in a sample nucleic acid sequence, comprising: computer code that receives a plurality of signals corresponding to probe intensities for a plurality of nucleic acid probes, each probe intensity indicating an extent of hybridization of a nucleic acid probe with said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that calculates a ratio of a higher probe intensity to a lower probe intensity; computer code that generates a base call identifying said unknown base according to a base of a nucleic acid probe having said higher probe intensity if said ratio is greater than a predetermined ratio value; and a computer readable medium that stores said computer codes.
Claim 4
Dependent Claim
128 words
A computer program product that identifies an unknown base in a sample nucleic acid sequence, comprising: computer code that receives a plurality of signals corresponding to probe intensities for a plurality of nucleic acid probes, each probe intensity indicating an extent of hybridization of a nucleic acid probe with said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that calculates a ratio of a higher probe intensity to a lower probe intensity; computer code that generates a base call identifying said unknown base according to a base of a nucleic acid probe having said higher probe intensity if said ratio is greater than a predetermined ratio value; and a computer readable medium that stores said computer codes.
Claim 5
Dependent Claim
188 words
A computer program product that identifies an unknown base in a sample nucleic acid sequence, comprising: computer code that receives a first set of signals corresponding to a first set of probe intensities, each probe intensity in said first set indicating an extent of hybridization of a nucleic acid probe with a reference nucleic acid sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that receives a second set of signals corresponding to a second set of probe intensities, each probe intensity in said second set indicating an extent of hybridization of a nucleic acid probe with said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that performs a comparison of at least one of said probe intensities in said first set and at least one of said probe intensities in said second set; computer code that generates a base call identifying said unknown base according to results of said comparisons said sequence of said nucleic acid probe; and a computer readable medium that stores said computer codes.
Claim 6
Dependent Claim
188 words
A computer program product that identifies an unknown base in a sample nucleic acid sequence, comprising: computer code that receives a first set of signals corresponding to a first set of probe intensities, each probe intensity in said first set indicating an extent of hybridization of a nucleic acid probe with a reference nucleic acid sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that receives a second set of signals corresponding to a second set of probe intensities, each probe intensity in said second set indicating an extent of hybridization of a nucleic acid probe with said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that performs a comparison of at least one of said probe intensities in said first set and at least one of said probe intensities in said second set; computer code that generates a base call identifying said unknown base according to results of said comparisons said sequence of said nucleic acid probe; and a computer readable medium that stores said computer codes.
Claim 7
Dependent Claim
168 words
A computer program product that identifies an unknown base in a sample nucleic acid sequence, comprising: computer code that receives signals corresponding to statistics about a plurality of experiments, each of said experiments producing probe intensities, each probe intensity indicating an extent of hybridization of a nucleic acid probe with a reference nucleic acid sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that receives a plurality of signals corresponding to probe intensities, each probe intensity indicating an extent of hybridization of a nucleic acid probe with said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that performs a comparison of at least one of said plurality of probe intensities with said statistics; computer code that generates a base call identifying said unknown base according to results of said comparison and said sequence of said nucleic acid probe; and a computer readable medium that stores said computer codes.
Claim 8
Dependent Claim
168 words
A computer program product that identifies an unknown base in a sample nucleic acid sequence, comprising: computer code that receives signals corresponding to statistics about a plurality of experiments, each of said experiments producing probe intensities, each probe intensity indicating an extent of hybridization of a nucleic acid probe with a reference nucleic acid sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that receives a plurality of signals corresponding to probe intensities, each probe intensity indicating an extent of hybridization of a nucleic acid probe with said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that performs a comparison of at least one of said plurality of probe intensities with said statistics; computer code that generates a base call identifying said unknown base according to results of said comparison and said sequence of said nucleic acid probe; and a computer readable medium that stores said computer codes.
Claim 9
Independent Claim
130 words
A system that identifies an unknown base in a sample nucleic acid sequence, comprising: a processor; and a computer readable medium coupled to said processor for storing a computer program comprising: computer code that receives a plurality of signals corresponding to probe intensities for a plurality of nucleic acid probes, each probe intensity indicating an extent of hybridization of a nucleic acid probe with at least one nucleic acid sequence including said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that performs a comparison of said plurality of probe intensities to each other; and computer code that generates a base call identifying said unknown base according to results of said comparison and said sequences of said nucleic acid probes.
Claim 10
Independent Claim
130 words
A system that identifies an unknown base in a sample nucleic acid sequence, comprising: a processor; and a computer readable medium coupled to said processor for storing a computer program comprising: computer code that receives a plurality of signals corresponding to probe intensities for a plurality of nucleic acid probes, each probe intensity indicating an extent of hybridization of a nucleic acid probe with at least one nucleic acid sequence including said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that performs a comparison of said plurality of probe intensities to each other; and computer code that generates a base call identifying said unknown base according to results of said comparison and said sequences of said nucleic acid probes.
Claim 11
Independent Claim
134 words
A system that identifies an unknown base in a sample nucleic acid sequence, comprising: a processor; and a computer readable medium coupled to said processor for storing a computer program comprising: computer code that receives a plurality of signals corresponding to probe intensities for a plurality of nucleic acid probes, each probe intensity indicating an extent of hybridization of a nucleic acid probe with said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that calculates a ratio of a higher probe intensity to a lower probe intensity; and computer code that generates a base call identifying said unknown base according to a base of a nucleic acid probe having said higher probe intensity if said ratio is greater than a predetermined ratio value.
Claim 12
Independent Claim
134 words
A system that identifies an unknown base in a sample nucleic acid sequence, comprising: a processor; and a computer readable medium coupled to said processor for storing a computer program comprising: computer code that receives a plurality of signals corresponding to probe intensities for a plurality of nucleic acid probes, each probe intensity indicating an extent of hybridization of a nucleic acid probe with said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that calculates a ratio of a higher probe intensity to a lower probe intensity; and computer code that generates a base call identifying said unknown base according to a base of a nucleic acid probe having said higher probe intensity if said ratio is greater than a predetermined ratio value.
Claim 13
Independent Claim
186 words
A system that identifies an unknown base in a sample nucleic acid sequence, comprising: a processor; and a computer readable medium coupled to said processor for storing a computer program comprising: computer code that receives a first set of signals corresponding to probe intensities, each probe intensity in said first set indicating an extent of hybridization of a nucleic acid probe with a reference nucleic acid sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that receives a second set of signals corresponding to probe intensities, each probe intensity in said second set indicating an extent of hybridization of a nucleic acid probe with said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that performs a comparison of at least one of said probe intensities in said first set and at least one of said probe intensities in said second set; and computer code that generates a base call identifying said unknown base according to results of said comparison and said sequence of nucleic acid probe.
Claim 14
Independent Claim
186 words
A system that identifies an unknown base in a sample nucleic acid sequence, comprising: a processor; and a computer readable medium coupled to said processor for storing a computer program comprising: computer code that receives a first set of signals corresponding to probe intensities, each probe intensity in said first set indicating an extent of hybridization of a nucleic acid probe with a reference nucleic acid sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that receives a second set of signals corresponding to probe intensities, each probe intensity in said second set indicating an extent of hybridization of a nucleic acid probe with said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that performs a comparison of at least one of said probe intensities in said first set and at least one of said probe intensities in said second set; and computer code that generates a base call identifying said unknown base according to results of said comparison and said sequence of nucleic acid probe.
Claim 15
Independent Claim
174 words
A system that identifies an unknown base in a sample nucleic acid sequence, comprising: a processor; and a computer readable medium coupled to said processor for storing a computer program comprising: computer code that receives signals corresponding to statistics about a plurality of experiments, each of said experiments producing probe intensities, each probe intensity indicating an extent of hybridization of a nucleic acid probe with a reference nucleic acid sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that receives a plurality of signals corresponding to probe intensities, each probe intensity indicating an extent of hybridization of a nucleic acid probe with said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that performs a comparison of at least one of said plurality of probe intensities with said statistics; and computer code that generates a base call identifying said unknown base according to results of said comparison and said sequence of said nucleic acid probe.
Claim 16
Independent Claim
174 words
A system that identifies an unknown base in a sample nucleic acid sequence, comprising: a processor; and a computer readable medium coupled to said processor for storing a computer program comprising: computer code that receives signals corresponding to statistics about a plurality of experiments, each of said experiments producing probe intensities, each probe intensity indicating an extent of hybridization of a nucleic acid probe with a reference nucleic acid sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that receives a plurality of signals corresponding to probe intensities, each probe intensity indicating an extent of hybridization of a nucleic acid probe with said sample sequence, and each nucleic acid probe differing from each other by at least a single base; computer code that performs a comparison of at least one of said plurality of probe intensities with said statistics; and computer code that generates a base call identifying said unknown base according to results of said comparison and said sequence of said nucleic acid probe.
Claim 17
Independent Claim
23 words
A system according to claims 5, 6, 7, or 8, wherein the plurality of nucleic acid probes are in an array of probes.
Claim 18
Independent Claim
19 words
A system according to claims 5, 6, 7, or 8, wherein the plurality of probe intensities are fluorescent intensities.
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USPTO Annuity & Maintenance Windows
| Annuity Stage | Window Opens | Payment Deadline | Surcharge Period Until | Estimated Fee | Status |
|---|---|---|---|---|---|
| 3.5 Years (Year 4) | 2001-08-17 | 2002-02-16 | 2002-08-18 | $2000.00 | Window Closed / Lapsed |
| 7.5 Years (Year 8) | 2005-08-17 | 2006-02-16 | 2006-08-18 | $3760.00 | Window Closed / Lapsed |
| 11.5 Years (Year 12) | 2009-08-17 | 2010-02-16 | 2010-08-18 | $7700.00 | Window Closed / Lapsed |