Title: Methods for rule-based genome design

Abstract

Methods and systems for designing, testing, and validating genome designs based on rules or constraints or conditions or parameters or features and scoring are described herein. A computer-implemented method includes receiving data for a known genome and a list of alleles, identifying and removing occurrences of each allele in the known genome, determining a plurality of allele choices with which to replace occurrences in the known genome, generating a plurality of alternative gene sequences for a genome design based on the known genome, wherein each alternative gene sequence comprises a different allele choice, applying a plurality of rules or constraints or conditions or parameters or features to each alternative gene sequence by assigning a score for each rule or constraint or condition or parameter or feature in each alternative gene sequence, resulting in scores for the applied plurality of rules or constraints or conditions or parameters or features, scoring each alternative gene sequence based on a weighted combination of the scores for the plurality of rules or constraints or conditions or parameters or features, and selecting at least one alternative gene sequence as the genome design based on the scoring.

Inventors:

Kuznetsov, Gleb; Lajoie, Marc J.; Landon, Matthieu M.; Napolitano, Michael G.; Goodman, Daniel Bryan; Gregg, Christopher J.; Church, George M.; Ostrov, Nili

Issue Date:

2022-06-14

Research Org.:

Harvard Univ., Cambridge, MA (United States)

Sponsoring Org.:

USDOE

OSTI Identifier:

1893038

Patent Number(s):

11361845

Application Number:

16/309,645

Assignee:

President and Fellows of Harvard College (Cambridge, MA)

Patent Classifications (CPCs):

A - HUMAN NECESSITIES A61 - MEDICAL OR VETERINARY SCIENCE A61K - PREPARATIONS FOR MEDICAL, DENTAL, OR TOILET PURPOSES

C - CHEMISTRY C07 - ORGANIC CHEMISTRY C07K - PEPTIDES

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A - HUMAN NECESSITIES A61 - MEDICAL OR VETERINARY SCIENCE A61K - PREPARATIONS FOR MEDICAL, DENTAL, OR TOILET PURPOSES

A61K38/00 - Medicinal preparations containing peptides

C - CHEMISTRY C07 - ORGANIC CHEMISTRY C07K - PEPTIDES

C07K14/245 - Escherichia

C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES

C12N15/1089 - {Design, preparation, screening or analysis of libraries using computer algorithms}

C - CHEMISTRY C12 - BIOCHEMISTRY C12P - FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE {

C12P21/00 - Preparation of peptides or proteins

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

G16B20/50 - Mutagenesis
G16B35/10 - Design of libraries

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DOE Contract Number:  

FG02-02ER63445; HR0011-13-1-0002

Resource Type:

Patent

Resource Relation:

Patent File Date: 06/15/2017

Country of Publication:

United States

Language:

English