Title: Computer-aided visualization and analysis system for sequence evaluation

Abstract

A computer system (1) 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 may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area (814) and sample sequences in another area (816) on a display device (3).

Inventors:

Chee, Mark S ^[1]

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+ Show Inventor Affiliations

1. Palo Alto, CA

Issue Date:

1999-10-26

Research Org.:

Affymetrix, Inc. (Santa Clara, CA)

OSTI Identifier:

872618

Patent Number(s):

5974164

Application Number:

5974164

Assignee:

Affymetrix, Inc. (Santa Clara, CA)

Patent Classifications (CPCs):

B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01J - CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY

G - PHYSICS G16 - INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS G16B - BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

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B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01J - CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY

B01J2219/00617 - by chemical means

G - PHYSICS G16 - INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS G16B - BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

G16B25/00 - ICT specially adapted for hybridisation

B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01J - CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY

B01J2219/00722 - Nucleotides
B01J2219/00695 - Synthesis control routines, e.g. using computer programs
B01J2219/0061 - The surface being organic
B01J2219/00612 - the surface being inorganic
B01J2219/00689 - using computers

B - PERFORMING OPERATIONS B82 - NANOTECHNOLOGY B82Y - SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES

B82Y30/00 - Nanotechnology for materials or surface science, e.g. nanocomposites

G - PHYSICS G16 - INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS G16B - BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

G16B30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

C12Q1/6874 - involving nucleic acid arrays, e.g. sequencing by hybridisation

C - CHEMISTRY C40 - COMBINATORIAL TECHNOLOGY C40B - COMBINATORIAL CHEMISTRY

C40B60/14 - for creating libraries
C40B40/06 - Libraries containing nucleotides or polynucleotides, or derivatives thereof

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

C12Q1/68 - involving nucleic acids

G - PHYSICS G01 - MEASURING G01N - INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES

G01N15/1475 - {using image analysis for extracting features of the particle}

B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01J - CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY

B01J2219/00659 - Two-dimensional arrays
B01J2219/00608 - DNA chips
B01J2219/00529 - DNA chips
B01J2219/00711 - Light-directed synthesis
B01J19/0046 - {Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides
B01J2219/00626 - Covalent
B01J2219/00432 - Photolithographic masks

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

C12Q1/6827 - for detection of mutation or polymorphism

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DOE Contract Number:  

FG03-92ER81275

Resource Type:

Patent

Country of Publication:

United States

Language:

English

Subject:

computer-aided; visualization; analysis; sequence; evaluation; computer; analyzing; nucleic; acid; sequences; provided; perform; multiple; methods; determining; bases; fluorescence; intensities; hybridized; probes; results; individual; experiments; improved; processing; comparative; displaying; reference; 814; sample; 816; display; device; comparative analysis; reference sequence; acid probes; acid sequence; nucleic acid; acid sequences; acid probe; display device; sequence evaluation; sample sequences; analyzing nucleic; processing nucleic; multiple experiments; multiple methods; computer-aided visualization; reference sequences; perform multiple; fluorescence intensities; form multiple; displaying reference; individual experiments; hybridized nucleic; /382/435/999/