Computer-aided engineering system for design of sequence arrays and lithographic masks
AssigneeAffymetrix, Inc.
InventorsEarl A. Hubbell, Robert J. Lipshutz, Macdonald S. Morris, James L. Winkler
Life of this patent
Estimating the term…
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.
Claims16
A method of designing a synthesis method for an array of materials to be synthesized on a substrate, said array formed from groups of diverse biological materials, comprising the steps of:
- inputting genetic sequences to a design computer system;
- determining a sequence of monomer additions used to form said genetic sequences in said computer by the steps of:
- identifying a monomer addition template;
- and
- for monomer additions in said template, determining if said monomer additions are needed in formation of said genetic sequence and, if not, removing said monomer additions from said template;
- generating an output file comprising a series of desired monomer additions not removed from said template;
- and
- providing said series of monomer additions as an input file to a synthesizer.
A method of designing and using a synthesis sequence for a biological polymer comprising the steps of:
- in a programmed digital computer, identifying a series of monomer additions for adjacent synthesis regions on a substrate;
- adjusting said series of monomer additions to reduce the number of monomer additions that differ between at least two adjacent synthesis regions;
- and
- using said adjusted series of monomer additions to form said substrate.
A method of designing an array and its method of synthesis comprising the steps of:
- in a computer system:
- inputting a genetic sequence file;
- identifying locations in said array for formation of genetic probes corresponding to said genetic sequence and selected mutations thereof;
- determining a sequence of monomer additions for formation of said probes and said selected mutations thereof;
- outputting at least one computer file representing said locations and said sequence of monomer additions;
- and
- using said at least one computer file to form said array.
Dependencies are inferred from the claim text.