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1. WO2017218727 - METHODS FOR RULE-BASED GENOME DESIGN

Publication Number WO/2017/218727
Publication Date 21.12.2017
International Application No. PCT/US2017/037596
International Filing Date 15.06.2017
IPC
C12N 15/10 2006.1
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
15Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
09Recombinant DNA-technology
10Processes for the isolation, preparation or purification of DNA or RNA
C12N 15/09 2006.1
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
15Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
09Recombinant DNA-technology
C12Q 1/68 2006.1
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
68involving nucleic acids
G06F 19/22 2011.1
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
FELECTRIC DIGITAL DATA PROCESSING
19Digital computing or data processing equipment or methods, specially adapted for specific applications
10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
22for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism discovery or sequence alignment
CPC
A61K 38/00
AHUMAN NECESSITIES
61MEDICAL OR VETERINARY SCIENCE; HYGIENE
KPREPARATIONS FOR MEDICAL, DENTAL, OR TOILET PURPOSES
38Medicinal preparations containing peptides
C07K 14/245
CCHEMISTRY; METALLURGY
07ORGANIC CHEMISTRY
KPEPTIDES
14Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
195from bacteria
24from Enterobacteriaceae (F), e.g. Citrobacter, Serratia, Proteus, Providencia, Morganella, Yersinia
245Escherichia (G)
C12N 15/1089
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
15Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
09Recombinant DNA-technology
10Processes for the isolation, preparation or purification of DNA or RNA
1034Isolating an individual clone by screening libraries
1089Design, preparation, screening or analysis of libraries using computer algorithms
C12P 21/00
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
PFERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
21Preparation of peptides or proteins
G16B 20/50
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
20ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
50Mutagenesis
G16B 35/10
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
35ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
10Design of libraries
Applicants
  • PRESIDENT AND FELLOWS OF HARVARD COLLEGE [US]/[US]
Inventors
  • KUZNETSOV, Gleb
  • LAJOIE, Marc J.
  • LANDON, Matthieu M.
  • NAPOLITANO, Michael G.
  • GOODMAN, Daniel Bryan
  • GREGG, Christopher J.
  • CHURCH, George M.
  • OSTROV, Nili
Agents
  • IWANICKI, John P.
Priority Data
62/350,46815.06.2016US
Publication Language English (en)
Filing Language English (EN)
Designated States
Title
(EN) METHODS FOR RULE-BASED GENOME DESIGN
(FR) PROCÉDÉS DE CONCEPTION D'UN GÉNOME SUR LA BASE DE RÈGLES
Abstract
(EN) Methods and systems for designing, testing, and validating genome designs 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, 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, scoring each alternative gene sequence based on a weighted combination of the scores, and selecting at least one alternative gene sequence as the genome design based on the scoring.
(FR) L'invention concerne des procédés et des systèmes de conception, test et validation de conceptions d'un génome. Un procédé informatisé comprend les étapes consistant à : recevoir des données relatives à un génome connu et à une liste d'allèles; identifier et éliminer les occurrences de chaque allèle dans le génome connu; déterminer une pluralité de choix d'allèles permettant de remplacer les occurrences dans le génome connu; générer une pluralité d'autres séquences de gènes permettant une conception d'un génome sur la base du génome connu; appliquer une pluralité de règles, contraintes, conditions, paramètres ou caractéristiques à chaque autre séquence de gènes en attribuant une note à chaque règle, contrainte, condition, paramètre ou caractéristique dans chaque autre séquence de gènes; obtenir des notes; noter chaque autre séquence de gènes sur la base d'une combinaison pondérée des notes; et sélectionner au moins une autre séquence de gènes au titre de la conception du génome sur la base de la notation.
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