SG11201811025VA - Systems and methods for automated annotation and screening of biological sequences - Google Patents

Systems and methods for automated annotation and screening of biological sequences

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Publication number
SG11201811025VA
SG11201811025VA SG11201811025VA SG11201811025VA SG11201811025VA SG 11201811025V A SG11201811025V A SG 11201811025VA SG 11201811025V A SG11201811025V A SG 11201811025VA SG 11201811025V A SG11201811025V A SG 11201811025VA SG 11201811025V A SG11201811025V A SG 11201811025VA
Authority
SG
Singapore
Prior art keywords
international
screening
california
applicant
community
Prior art date
Application number
SG11201811025VA
Inventor
James Diggans
Original Assignee
Twist Bioscience Corp
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Twist Bioscience Corp filed Critical Twist Bioscience Corp
Publication of SG11201811025VA publication Critical patent/SG11201811025VA/en

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Classifications

    • 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

Abstract

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property 11111110111101110101011111010111110 0101110101111110011111111111111# 1111 Organization International Bureau (10) International Publication Number 0 (43) International Publication Date .....0\"\" WO 2017/214574 Al 14 December 2017 (14.12.2017) W I PO I PC T (51) International Patent GO6F 17/50 (2006.01) GO6F 19/22 (2011.01) (21) International Application (22) International Filing Date: (25) Filing Language: (26) Publication Language: (30) Priority Data: 62/348,786 10 62/375,858 16 (71) Applicant: TWIST [US/US]; 455 Mission Francisco, California 94158 Classification: (72) Inventor: DIGGANS, James; 1324 Cordilleras Avenue, G06F 19/28 (2011.01) San Carlos, California 94070 (US). C12N 15/10 (2006.01) (74) Agent: HARBURGER, David; WILSON SONSINI Number: GOODRICH & ROSATI, 650 Page Mill Road, Palo Alto, PCT/US2017/036868 California 94304 (US). (81) Designated States (unless otherwise indicated, for every 09 June 2017 (09.06.2017) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, English CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, English DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, June 2016 (10.06.2016) US KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, August 2016 (16.08.2016) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NE NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, BIOSCIENCE CORPORATION SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, Bay Boulevard South, Suite 545, San TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (US). METHODS FOR AUTOMATED ANNOTATION AND SCREENING OF BIOLOGICAL SEQUENCES knowledge and participa- science on the link to broaden both interest empowered to evaluate the described herein provide biological sequences from (54) Title: SYSTEMS AND Query File Protein database multiple or In Blast Report Restricted lists Restricted lists disclosure describes software tools for effective biosecurity herein provide assistance and negative outcomes. Screening so that practitioners and biological sequence than waiting until synthesis or even expression. across the same or based on community community to track emerging enables the community construct providers are addition, screening tools associated with harmful Screen report FIG. 3A to the synthetic biology tools described herein orders for sequences ,-, 7 r (57) : The present IN in tion. Annotation tools described 71. between individual proteins N and effective practice of biosecurity ---, safety of order requests rather I N for screening of polynucleotides 1-1 C a reference database. ei C [Continued on next page] WO 2017/214574 Al MIDEDIMOMOIDEIRMEM0011010HEINEHMEMOIMIE (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Declarations under Rule 4.17: — as to applicant's entitlement to apply for and be granted a patent (Rule 4.17(ii)) — as to the applicant's entitlement to claim the priority of the earlier application (Rule 4.17(iii)) Published: — with international search report (Art. 21(3))
SG11201811025VA 2016-06-10 2017-06-09 Systems and methods for automated annotation and screening of biological sequences SG11201811025VA (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201662348786P 2016-06-10 2016-06-10
US201662375858P 2016-08-16 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
SG11201811025VA true SG11201811025VA (en) 2019-01-30

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SG11201811025VA SG11201811025VA (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 (en)
EP (1) EP3469499A4 (en)
JP (2) JP2019523940A (en)
KR (1) KR102476915B1 (en)
CN (1) CN109564769A (en)
CA (1) CA3027127A1 (en)
SG (1) SG11201811025VA (en)
WO (1) WO2017214574A1 (en)

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EP3722442B1 (en) 2013-08-05 2023-04-05 Twist Bioscience Corporation De novo synthesized gene libraries
WO2016126882A1 (en) 2015-02-04 2016-08-11 Twist Bioscience Corporation Methods and devices for de novo oligonucleic acid assembly
WO2016172377A1 (en) 2015-04-21 2016-10-27 Twist Bioscience Corporation Devices and methods for oligonucleic acid library synthesis
WO2017049231A1 (en) 2015-09-18 2017-03-23 Twist Bioscience Corporation Oligonucleic acid variant libraries and synthesis thereof
KR20180058772A (en) 2015-09-22 2018-06-01 트위스트 바이오사이언스 코포레이션 Flexible substrate for nucleic acid synthesis
US9895673B2 (en) 2015-12-01 2018-02-20 Twist Bioscience Corporation Functionalized surfaces and preparation thereof
JP6854340B2 (en) 2016-08-22 2021-04-07 ツイスト バイオサイエンス コーポレーション Denovo Synthesized Nucleic Acid Library
CN110248724B (en) 2016-09-21 2022-11-18 特韦斯特生物科学公司 Nucleic acid based data storage
AU2017378492B2 (en) 2016-12-16 2022-06-16 Twist Bioscience Corporation Variant libraries of the immunological synapse and synthesis thereof
SG11201907713WA (en) 2017-02-22 2019-09-27 Twist Bioscience Corp Nucleic acid based data storage
AU2018234629A1 (en) 2017-03-15 2019-10-17 Twist Bioscience Corporation Variant libraries of the immunological synapse and synthesis thereof
WO2018231864A1 (en) 2017-06-12 2018-12-20 Twist Bioscience Corporation Methods for seamless nucleic acid assembly
KR102628876B1 (en) 2017-06-12 2024-01-23 트위스트 바이오사이언스 코포레이션 Methods for seamless nucleic acid assembly
WO2019051501A1 (en) 2017-09-11 2019-03-14 Twist Bioscience Corporation Gpcr binding proteins and synthesis thereof
KR102637566B1 (en) 2017-10-20 2024-02-16 트위스트 바이오사이언스 코포레이션 Heated nanowells for polynucleotide synthesis
US10936953B2 (en) 2018-01-04 2021-03-02 Twist Bioscience Corporation DNA-based digital information storage with sidewall electrodes
AU2019270243A1 (en) 2018-05-18 2021-01-07 Twist Bioscience Corporation Polynucleotides, reagents, and methods for nucleic acid hybridization
US11232852B2 (en) 2018-12-06 2022-01-25 Battelle Memorial Institute Technologies for nucleotide sequence screening
WO2020176680A1 (en) 2019-02-26 2020-09-03 Twist Bioscience Corporation Variant nucleic acid libraries for antibody optimization
EP3930753A4 (en) 2019-02-26 2023-03-29 Twist Bioscience Corporation Variant nucleic acid libraries for glp1 receptor
WO2020257612A1 (en) 2019-06-21 2020-12-24 Twist Bioscience Corporation Barcode-based nucleic acid sequence assembly

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Publication number Publication date
WO2017214574A1 (en) 2017-12-14
EP3469499A1 (en) 2019-04-17
US20170357752A1 (en) 2017-12-14
CN109564769A (en) 2019-04-02
KR20190017932A (en) 2019-02-20
JP2019523940A (en) 2019-08-29
KR102476915B1 (en) 2022-12-12
JP2022181213A (en) 2022-12-07
EP3469499A4 (en) 2020-10-21
CA3027127A1 (en) 2017-12-14

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