CA3027127A1 - Systems and methods for automated annotation and screening of biological sequences - Google Patents

Systems and methods for automated annotation and screening of biological sequences Download PDF

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Publication number
CA3027127A1
CA3027127A1 CA3027127A CA3027127A CA3027127A1 CA 3027127 A1 CA3027127 A1 CA 3027127A1 CA 3027127 A CA3027127 A CA 3027127A CA 3027127 A CA3027127 A CA 3027127A CA 3027127 A1 CA3027127 A1 CA 3027127A1
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Prior art keywords
biological
sequences
sequence
harmful
instructions
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Pending
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CA3027127A
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English (en)
French (fr)
Inventor
James Diggans
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Twist Bioscience Corp
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Twist Bioscience Corp
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Publication of CA3027127A1 publication Critical patent/CA3027127A1/en
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    • 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
    • G16B30/10—Sequence alignment; Homology search
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1068—Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1089—Design, preparation, screening or analysis of libraries using computer algorithms
    • G—PHYSICS
    • G05—CONTROLLING; REGULATING
    • G05B—CONTROL OR REGULATING SYSTEMS IN GENERAL; FUNCTIONAL ELEMENTS OF SUCH SYSTEMS; MONITORING OR TESTING ARRANGEMENTS FOR SUCH SYSTEMS OR ELEMENTS
    • G05B15/00—Systems controlled by a computer
    • 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
    • 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
    • G16B30/20—Sequence assembly
    • 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
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • 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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • 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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/30—Data warehousing; Computing architectures
    • 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
    • G16B99/00—Subject matter not provided for in other groups of this subclass
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Theoretical Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • General Engineering & Computer Science (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Biomedical Technology (AREA)
  • Organic Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Microbiology (AREA)
  • Bioethics (AREA)
  • Databases & Information Systems (AREA)
  • Library & Information Science (AREA)
  • General Physics & Mathematics (AREA)
  • Automation & Control Theory (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
CA3027127A 2016-06-10 2017-06-09 Systems and methods for automated annotation and screening of biological sequences Pending CA3027127A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201662348786P 2016-06-10 2016-06-10
US62/348,786 2016-06-10
US201662375858P 2016-08-16 2016-08-16
US62/375,858 2016-08-16
PCT/US2017/036868 WO2017214574A1 (en) 2016-06-10 2017-06-09 Systems and methods for automated annotation and screening of biological sequences

Publications (1)

Publication Number Publication Date
CA3027127A1 true CA3027127A1 (en) 2017-12-14

Family

ID=60574009

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3027127A Pending CA3027127A1 (en) 2016-06-10 2017-06-09 Systems and methods for automated annotation and screening of biological sequences

Country Status (8)

Country Link
US (1) US20170357752A1 (enExample)
EP (1) EP3469499A4 (enExample)
JP (2) JP2019523940A (enExample)
KR (1) KR102476915B1 (enExample)
CN (1) CN109564769A (enExample)
CA (1) CA3027127A1 (enExample)
SG (1) SG11201811025VA (enExample)
WO (1) WO2017214574A1 (enExample)

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US9981239B2 (en) 2015-04-21 2018-05-29 Twist Bioscience Corporation Devices and methods for oligonucleic acid library synthesis
KR20180050411A (ko) 2015-09-18 2018-05-14 트위스트 바이오사이언스 코포레이션 올리고핵산 변이체 라이브러리 및 그의 합성
CN108698012A (zh) 2015-09-22 2018-10-23 特韦斯特生物科学公司 用于核酸合成的柔性基底
WO2017095958A1 (en) 2015-12-01 2017-06-08 Twist Bioscience Corporation Functionalized surfaces and preparation thereof
KR102212257B1 (ko) 2016-08-22 2021-02-04 트위스트 바이오사이언스 코포레이션 드 노보 합성된 핵산 라이브러리
WO2018057526A2 (en) 2016-09-21 2018-03-29 Twist Bioscience Corporation Nucleic acid based data storage
EP3554514A4 (en) 2016-12-16 2020-08-05 Twist Bioscience Corporation BANKS OF VARIANTS OF IMMUNOLOGICAL SYNAPSE AND THEIR SYNTHESIS
CN110892485B (zh) 2017-02-22 2024-03-22 特韦斯特生物科学公司 基于核酸的数据存储
AU2018234629A1 (en) 2017-03-15 2019-10-17 Twist Bioscience Corporation Variant libraries of the immunological synapse and synthesis thereof
JP7169999B2 (ja) 2017-06-12 2022-11-11 ツイスト バイオサイエンス コーポレーション シームレス核酸アセンブリのための方法
WO2018231864A1 (en) 2017-06-12 2018-12-20 Twist Bioscience Corporation Methods for seamless nucleic acid assembly
AU2018328847A1 (en) 2017-09-11 2020-04-23 Twist Bioscience Corporation GPCR binding proteins and synthesis thereof
WO2019079769A1 (en) 2017-10-20 2019-04-25 Twist Bioscience Corporation HEATED NANOWELLS FOR THE SYNTHESIS OF POLYNUCLEOTIDES
EP4715681A2 (en) 2018-01-04 2026-03-25 Atlas Data Storage, Inc. Dna-based digital information storage
IL278771B2 (en) 2018-05-18 2025-09-01 Twist Bioscience Corp Polynucleotides, reagents and methods for nucleic acid hybridization
EP3891280A4 (en) * 2018-12-06 2022-08-10 Battelle Memorial Institute TECHNOLOGIES FOR NUCLEOTIDE SEQUENCE SCREENING
WO2020139871A1 (en) 2018-12-26 2020-07-02 Twist Bioscience Corporation Highly accurate de novo polynucleotide synthesis
WO2020176678A1 (en) 2019-02-26 2020-09-03 Twist Bioscience Corporation Variant nucleic acid libraries for glp1 receptor
AU2020227802A1 (en) 2019-02-26 2021-10-14 Twist Bioscience Corporation Variant nucleic acid libraries for antibody optimization
CA3144644A1 (en) 2019-06-21 2020-12-24 Twist Bioscience Corporation Barcode-based nucleic acid sequence assembly
US12091777B2 (en) 2019-09-23 2024-09-17 Twist Bioscience Corporation Variant nucleic acid libraries for CRTH2
EP4034564A4 (en) 2019-09-23 2023-12-13 Twist Bioscience Corporation VARIANT NUCLEIC ACID LIBRARIES FOR SINGLE-DOMAIN ANTIBODIES
BR112022011235A2 (pt) 2019-12-09 2022-12-13 Twist Bioscience Corp Bibliotecas de variantes de ácido nucleico para receptores de adenosina
EP4073809A1 (en) * 2020-01-23 2022-10-19 Massachusetts Institute of Technology Methods of functionally screening biological sequence fragments
WO2021222316A2 (en) 2020-04-27 2021-11-04 Twist Bioscience Corporation Variant nucleic acid libraries for coronavirus
US12391762B2 (en) 2020-08-26 2025-08-19 Twist Bioscience Corporation Methods and compositions relating to GLP1R variants
CN117043171A (zh) 2020-08-28 2023-11-10 特韦斯特生物科学公司 用于合成的装置和方法
US11970697B2 (en) 2020-10-19 2024-04-30 Twist Bioscience Corporation Methods of synthesizing oligonucleotides using tethered nucleotides
EP4213158A1 (en) * 2020-11-13 2023-07-19 Ahead Biocomputing, Co. Ltd Information processing device, information processing method, recording medium recording information processing program, and information processing system
KR20230147617A (ko) 2021-01-21 2023-10-23 트위스트 바이오사이언스 코포레이션 아데노신 수용체에 관한 방법 및 조성물
US12258406B2 (en) 2021-03-24 2025-03-25 Twist Bioscience Corporation Antibodies that bind CD3 Epsilon
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WO2022271884A2 (en) 2021-06-22 2022-12-29 Twist Bioscience Corporation Methods and compositions relating to covid antibody epitopes
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Also Published As

Publication number Publication date
JP2019523940A (ja) 2019-08-29
WO2017214574A1 (en) 2017-12-14
KR102476915B1 (ko) 2022-12-12
CN109564769A (zh) 2019-04-02
SG11201811025VA (en) 2019-01-30
US20170357752A1 (en) 2017-12-14
EP3469499A1 (en) 2019-04-17
KR20190017932A (ko) 2019-02-20
JP2022181213A (ja) 2022-12-07
EP3469499A4 (en) 2020-10-21

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