Title: Computer-aided engineering system for design of sequence arrays and lithographic masks

Abstract

An improved set of computer tools for forming arrays. According to one aspect of the invention, a computer system is used to select probes and design the layout of an array of DNA or other polymers with certain beneficial characteristics. According to another aspect of the invention, a computer system uses chip design files to design and/or generate lithographic masks.

Inventors:

Hubbell, Earl A ^[1]; Lipshutz, Robert J ^[2]; Morris, Macdonald S ^[3]; Winkler, James L ^[2]

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+ Show Inventor Affiliations

1. Mt. View, CA
2. Palo Alto, CA
3. San Jose, CA

Issue Date:

1997-01-01

Research Org.:

Affymax Research Institute

OSTI Identifier:

870782

Patent Number(s):

5593839

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

C - CHEMISTRY C07 - ORGANIC CHEMISTRY C07K - PEPTIDES

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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

B01J2219/00722 - Nucleotides
B01J2219/00695 - Synthesis control routines, e.g. using computer programs

C - CHEMISTRY C07 - ORGANIC CHEMISTRY C07K - PEPTIDES

C07K1/045 - {using devices to improve synthesis, e.g. reactors, special vessels}

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

B01J2219/00612 - the surface being inorganic
B01J2219/00693 - Means for quality control
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

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

B01J2219/00637 - by coating it with another layer

C - CHEMISTRY C40 - COMBINATORIAL TECHNOLOGY C40B - COMBINATORIAL CHEMISTRY

C40B60/14 - for creating libraries

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

B01J2219/0059 - Sequential processes

C - CHEMISTRY C40 - COMBINATORIAL TECHNOLOGY C40B - COMBINATORIAL CHEMISTRY

C40B40/06 - Libraries containing nucleotides or polynucleotides, or derivatives thereof

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
B01J2219/00585 - Parallel processes
B01J2219/00529 - DNA chips
B01J2219/00711 - Light-directed synthesis
B01J19/0046 - {Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides
B01J2219/00596 - Solid-phase processes
B01J2219/00626 - Covalent
B01J2219/00432 - Photolithographic masks

C - CHEMISTRY C07 - ORGANIC CHEMISTRY C07K - PEPTIDES

C07K1/04 - on carriers {

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DOE Contract Number:  

FG03-92ER81275

Resource Type:

Patent

Country of Publication:

United States

Language:

English

Subject:

computer-aided; engineering; design; sequence; arrays; lithographic; masks; improved; set; computer; tools; forming; according; aspect; select; probes; layout; array; dna; polymers; beneficial; characteristics; chip; files; generate; lithographic masks; sequence arrays; select probes; beneficial characteristics; computer tools; computer-aided engineering; chip design; generate lithographic; design files; improved set; forming arrays; lithographic mask; /435/430/999/