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 PDFInfo
- 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
- Authority
- CA
- Canada
- Prior art keywords
- biological
- sequences
- sequence
- harmful
- instructions
- Prior art date
- Legal status (The legal status 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 status listed.)
- Pending
Links
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
Landscapes
- Life Sciences & Earth Sciences (AREA)
- Engineering & Computer Science (AREA)
- Health & Medical Sciences (AREA)
- Physics & Mathematics (AREA)
- Chemical & Material Sciences (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Biotechnology (AREA)
- General Health & Medical Sciences (AREA)
- Bioinformatics & Computational Biology (AREA)
- Biophysics (AREA)
- Theoretical Computer Science (AREA)
- Genetics & Genomics (AREA)
- General Engineering & Computer Science (AREA)
- Evolutionary Biology (AREA)
- Medical Informatics (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Wood Science & Technology (AREA)
- Biomedical Technology (AREA)
- Organic Chemistry (AREA)
- Zoology (AREA)
- Analytical Chemistry (AREA)
- Biochemistry (AREA)
- Molecular Biology (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Microbiology (AREA)
- Plant Pathology (AREA)
- Crystallography & Structural Chemistry (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)
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) |
Families Citing this family (39)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| SG11201600853UA (en) | 2013-08-05 | 2016-03-30 | Twist Bioscience Corp | De novo synthesized gene libraries |
| US10669304B2 (en) | 2015-02-04 | 2020-06-02 | Twist Bioscience Corporation | Methods and devices for de novo oligonucleic acid assembly |
| US9981239B2 (en) | 2015-04-21 | 2018-05-29 | Twist Bioscience Corporation | Devices and methods for oligonucleic acid library synthesis |
| EP3350314A4 (en) | 2015-09-18 | 2019-02-06 | Twist Bioscience Corporation | OLIGONUCLEIC ACID VARIANT LIBRARIES VARIANT AND SYNTHESIS THEREOF |
| KR102794025B1 (ko) | 2015-09-22 | 2025-04-09 | 트위스트 바이오사이언스 코포레이션 | 핵산 합성을 위한 가요성 기판 |
| CN115920796A (zh) | 2015-12-01 | 2023-04-07 | 特韦斯特生物科学公司 | 功能化表面及其制备 |
| EP3500672A4 (en) | 2016-08-22 | 2020-05-20 | Twist Bioscience Corporation | DE NOVO SYNTHETIZED NUCLEIC ACID LIBRARIES |
| US10417457B2 (en) | 2016-09-21 | 2019-09-17 | Twist Bioscience Corporation | Nucleic acid based data storage |
| GB2573069A (en) | 2016-12-16 | 2019-10-23 | Twist Bioscience Corp | Variant libraries of the immunological synapse and synthesis thereof |
| EP4556433A3 (en) | 2017-02-22 | 2025-08-06 | Twist Bioscience Corporation | Nucleic acid based data storage |
| WO2018170169A1 (en) | 2017-03-15 | 2018-09-20 | 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 |
| WO2018231872A1 (en) | 2017-06-12 | 2018-12-20 | Twist Bioscience Corporation | Methods for seamless nucleic acid assembly |
| US11407837B2 (en) | 2017-09-11 | 2022-08-09 | Twist Bioscience Corporation | GPCR binding proteins and synthesis thereof |
| CN111565834B (zh) | 2017-10-20 | 2022-08-26 | 特韦斯特生物科学公司 | 用于多核苷酸合成的加热的纳米孔 |
| KR102804057B1 (ko) | 2018-01-04 | 2025-05-07 | 트위스트 바이오사이언스 코포레이션 | Dna 기반 디지털 정보 저장 |
| CA3100739A1 (en) | 2018-05-18 | 2019-11-21 | Twist Bioscience Corporation | Polynucleotides, reagents, and methods for nucleic acid hybridization |
| WO2020118121A1 (en) | 2018-12-06 | 2020-06-11 | 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 |
| CN113766930B (zh) | 2019-02-26 | 2025-07-22 | 特韦斯特生物科学公司 | Glp1受体的变异核酸文库 |
| JP2022522668A (ja) | 2019-02-26 | 2022-04-20 | ツイスト バイオサイエンス コーポレーション | 抗体を最適化するための変異体核酸ライブラリ |
| US11332738B2 (en) | 2019-06-21 | 2022-05-17 | Twist Bioscience Corporation | Barcode-based nucleic acid sequence assembly |
| EP4034566A4 (en) | 2019-09-23 | 2024-01-24 | Twist Bioscience Corporation | VARIANT NUCLEIC ACID BANKS FOR CRTH2 |
| JP2022548783A (ja) | 2019-09-23 | 2022-11-21 | ツイスト バイオサイエンス コーポレーション | 単一ドメイン抗体のバリアント核酸ライブラリー |
| BR112022011235A2 (pt) | 2019-12-09 | 2022-12-13 | Twist Bioscience Corp | Bibliotecas de variantes de ácido nucleico para receptores de adenosina |
| US20230154569A1 (en) * | 2020-01-23 | 2023-05-18 | Massachusetts Institute Of Technology | Methods of functionality screening biological sequence fragments |
| MX2022013499A (es) | 2020-04-27 | 2023-01-16 | Twist Bioscience Corp | Bibliotecas de ácidos nucleicos variantes para coronavirus. |
| EP4204460A4 (en) | 2020-08-26 | 2024-09-25 | 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 |
| EP4229210A4 (en) | 2020-10-19 | 2025-01-08 | Twist Bioscience Corporation | METHOD FOR THE SYNTHESIS OF OLIGONUCLEOTIDES USING BOUND 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 |
| EP4314075A4 (en) | 2021-03-24 | 2025-04-09 | Twist Bioscience Corporation | VARIANT NUCLEIC ACID BANKS FOR CD3 |
| WO2022235584A1 (en) | 2021-05-03 | 2022-11-10 | Twist Bioscience Corporation | Variant nucleic acid libraries for glycans |
| US12201857B2 (en) | 2021-06-22 | 2025-01-21 | Twist Bioscience Corporation | Methods and compositions relating to covid antibody epitopes |
| WO2023023285A2 (en) | 2021-08-19 | 2023-02-23 | Twist Bioscience Corporation | Methods and compositions relating to covalently closed nucleic acids |
| WO2023069985A1 (en) * | 2021-10-19 | 2023-04-27 | Battelle Memorial Institute | Technologies for genetic engineering detection |
| US12134656B2 (en) | 2021-11-18 | 2024-11-05 | Twist Bioscience Corporation | Dickkopf-1 variant antibodies and methods of use |
| EP4460516A2 (en) | 2022-01-03 | 2024-11-13 | Twist Bioscience Corporation | Bispecific sars-cov-2 antibodies and methods of use |
Family Cites Families (9)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US5701256A (en) * | 1995-05-31 | 1997-12-23 | Cold Spring Harbor Laboratory | Method and apparatus for biological sequence comparison |
| WO2000049142A1 (de) * | 1999-02-19 | 2000-08-24 | Febit Ferrarius Biotechnology Gmbh | Verfahren zur herstellung von polymeren |
| CA2577741A1 (en) * | 2004-08-18 | 2006-03-02 | Abbott Molecular, Inc. | Determining data quality and/or segmental aneusomy using a computer system |
| WO2010025310A2 (en) * | 2008-08-27 | 2010-03-04 | Westend Asset Clearinghouse Company, Llc | Methods and devices for high fidelity polynucleotide synthesis |
| US20100292102A1 (en) * | 2009-05-14 | 2010-11-18 | Ali Nouri | System and Method For Preventing Synthesis of Dangerous Biological Sequences |
| EP2718862B1 (en) * | 2011-06-06 | 2018-10-31 | Koninklijke Philips N.V. | Method for assembly of nucleic acid sequence data |
| WO2013030827A1 (en) * | 2011-09-01 | 2013-03-07 | Genome Compiler Corporation | System for polynucleotide construct design, visualization and transactions to manufacture the same |
| US10347361B2 (en) * | 2012-10-24 | 2019-07-09 | Nantomics, Llc | Genome explorer system to process and present nucleotide variations in genome sequence data |
| SG11201600853UA (en) * | 2013-08-05 | 2016-03-30 | Twist Bioscience Corp | De novo synthesized gene libraries |
-
2017
- 2017-06-09 CA CA3027127A patent/CA3027127A1/en active Pending
- 2017-06-09 KR KR1020197000811A patent/KR102476915B1/ko active Active
- 2017-06-09 US US15/619,322 patent/US20170357752A1/en not_active Abandoned
- 2017-06-09 CN CN201780048980.4A patent/CN109564769A/zh active Pending
- 2017-06-09 WO PCT/US2017/036868 patent/WO2017214574A1/en not_active Ceased
- 2017-06-09 JP JP2018563706A patent/JP2019523940A/ja active Pending
- 2017-06-09 SG SG11201811025VA patent/SG11201811025VA/en unknown
- 2017-06-09 EP EP17811124.1A patent/EP3469499A4/en not_active Withdrawn
-
2022
- 2022-09-07 JP JP2022142326A patent/JP2022181213A/ja active Pending
Also Published As
| Publication number | Publication date |
|---|---|
| JP2019523940A (ja) | 2019-08-29 |
| WO2017214574A1 (en) | 2017-12-14 |
| US20170357752A1 (en) | 2017-12-14 |
| CN109564769A (zh) | 2019-04-02 |
| JP2022181213A (ja) | 2022-12-07 |
| EP3469499A4 (en) | 2020-10-21 |
| KR102476915B1 (ko) | 2022-12-12 |
| KR20190017932A (ko) | 2019-02-20 |
| EP3469499A1 (en) | 2019-04-17 |
| SG11201811025VA (en) | 2019-01-30 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| KR102476915B1 (ko) | 생물학적 서열의 자동화된 주석달기 및 스크리닝을 위한 시스템 및 방법 | |
| Tesson et al. | A comprehensive resource for exploring antiphage defense: DefenseFinder webservice, wiki and databases | |
| McGibbon et al. | MDTraj: a modern open library for the analysis of molecular dynamics trajectories | |
| US20200299684A1 (en) | Systems and methods for polynucleotide scoring | |
| Mulder et al. | Development of bioinformatics infrastructure for genomics research | |
| Glusman et al. | Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework | |
| Tang et al. | SynFind: compiling syntenic regions across any set of genomes on demand | |
| Priyadarshini et al. | Genome-based approaches to develop epitope-driven subunit vaccines against pathogens of infective endocarditis | |
| EP3063688A1 (en) | Visualization, sharing and analysis of large data sets | |
| Partin et al. | Learning curves for drug response prediction in cancer cell lines | |
| Vidanagamachchi et al. | Opportunities, challenges and future perspectives of using bioinformatics and artificial intelligence techniques on tropical disease identification using omics data | |
| Singh et al. | RUBICON: a framework for designing efficient deep learning-based genomic basecallers | |
| Xiao et al. | Challenges, solutions, and quality metrics of personal genome assembly in advancing precision medicine | |
| Chen et al. | Extension of SEIR compartmental models for constructive Lyapunov control of COVID-19 and analysis in terms of practical stability | |
| Lvovs et al. | Balancing ethical data sharing and open science for reproducible research in biomedical data science | |
| Pathak et al. | FisOmics: A portal of fish genomic resources | |
| Sarwar et al. | Database search, alignment viewer and genomics analysis tools: big data for bioinformatics | |
| US12512209B2 (en) | Systems and methods for medical imaging gateways | |
| Ahmed | Genomics and bioinformatics: integrating data for better genetic insights | |
| Holsten et al. | hCoCena: A toolbox for network-based co-expression analysis and horizontal integration of transcriptomic datasets | |
| Kumar et al. | AGeS: a software system for microbial genome sequence annotation | |
| Knoben et al. | Improving performance of hardware accelerators by optimizing data movement: A bioinformatics case study | |
| Cheng et al. | PyNCBIminer: A platform for assembling phylogenetic data sets via GenBank datamining | |
| Radig et al. | Tracking biological hallucinations in single-cell perturbation predictions using scArchon, a comprehensive benchmarking platform | |
| HK40005967A (en) | Systems and methods for automated annotation and screening of biological sequences |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| EEER | Examination request |
Effective date: 20220519 |