CA2863524A1 - Data analysis of dna sequences - Google Patents
Data analysis of dna sequences Download PDFInfo
- Publication number
- CA2863524A1 CA2863524A1 CA2863524A CA2863524A CA2863524A1 CA 2863524 A1 CA2863524 A1 CA 2863524A1 CA 2863524 A CA2863524 A CA 2863524A CA 2863524 A CA2863524 A CA 2863524A CA 2863524 A1 CA2863524 A1 CA 2863524A1
- Authority
- CA
- Canada
- Prior art keywords
- sequence
- sequences
- genome
- reference data
- data
- 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.)
- Abandoned
Links
- 238000007405 data analysis Methods 0.000 title abstract description 10
- 108091028043 Nucleic acid sequence Proteins 0.000 title description 8
- 238000004458 analytical method Methods 0.000 claims abstract description 132
- 108700019146 Transgenes Proteins 0.000 claims abstract description 113
- 238000000034 method Methods 0.000 claims abstract description 80
- 239000013604 expression vector Substances 0.000 claims abstract description 76
- 238000003780 insertion Methods 0.000 claims abstract description 49
- 230000037431 insertion Effects 0.000 claims abstract description 49
- 239000013599 cloning vector Substances 0.000 claims description 66
- 238000004422 calculation algorithm Methods 0.000 claims description 19
- 238000004364 calculation method Methods 0.000 claims description 16
- 238000011144 upstream manufacturing Methods 0.000 claims description 13
- 238000004451 qualitative analysis Methods 0.000 claims 2
- 238000004445 quantitative analysis Methods 0.000 claims 2
- 239000013615 primer Substances 0.000 description 103
- 230000010354 integration Effects 0.000 description 32
- 238000012163 sequencing technique Methods 0.000 description 24
- 239000013598 vector Substances 0.000 description 23
- 230000002829 reductive effect Effects 0.000 description 22
- 108020004414 DNA Proteins 0.000 description 19
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- 238000002869 basic local alignment search tool Methods 0.000 description 11
- 239000000523 sample Substances 0.000 description 10
- 238000004891 communication Methods 0.000 description 9
- 238000007481 next generation sequencing Methods 0.000 description 9
- 230000008569 process Effects 0.000 description 9
- 239000012634 fragment Substances 0.000 description 8
- 108090000623 proteins and genes Proteins 0.000 description 8
- 210000000349 chromosome Anatomy 0.000 description 7
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- 102000053602 DNA Human genes 0.000 description 5
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- 241000219195 Arabidopsis thaliana Species 0.000 description 1
- 239000003155 DNA primer Substances 0.000 description 1
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- 108091034117 Oligonucleotide Proteins 0.000 description 1
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- 238000012175 pyrosequencing Methods 0.000 description 1
- 238000011002 quantification Methods 0.000 description 1
- 108091008146 restriction endonucleases Proteins 0.000 description 1
- 238000007480 sanger sequencing Methods 0.000 description 1
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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
- 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
- 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
- G16B30/10—Sequence alignment; Homology search
-
- 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
- G16B50/10—Ontologies; Annotations
Landscapes
- Physics & Mathematics (AREA)
- Life Sciences & Earth Sciences (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Evolutionary Biology (AREA)
- General Health & Medical Sciences (AREA)
- Theoretical Computer Science (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Bioinformatics & Computational Biology (AREA)
- Biotechnology (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Biophysics (AREA)
- Medical Informatics (AREA)
- Bioethics (AREA)
- Databases & Information Systems (AREA)
- Chemical & Material Sciences (AREA)
- Analytical Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Management, Administration, Business Operations System, And Electronic Commerce (AREA)
Applications Claiming Priority (5)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201261596540P | 2012-02-08 | 2012-02-08 | |
| US61/596,540 | 2012-02-08 | ||
| US201261601090P | 2012-02-21 | 2012-02-21 | |
| US61/601,090 | 2012-02-21 | ||
| PCT/US2013/025087 WO2013119770A1 (en) | 2012-02-08 | 2013-02-07 | Data analysis of dna sequences |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CA2863524A1 true CA2863524A1 (en) | 2013-08-15 |
Family
ID=48946332
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA2863524A Abandoned CA2863524A1 (en) | 2012-02-08 | 2013-02-07 | Data analysis of dna sequences |
Country Status (13)
| Country | Link |
|---|---|
| US (1) | US20130211729A1 (enExample) |
| EP (1) | EP2812831A4 (enExample) |
| JP (1) | JP6314091B2 (enExample) |
| KR (1) | KR20140119723A (enExample) |
| CN (1) | CN104272311B (enExample) |
| AR (1) | AR089934A1 (enExample) |
| AU (1) | AU2013217079B2 (enExample) |
| BR (1) | BR112014019047A2 (enExample) |
| CA (1) | CA2863524A1 (enExample) |
| IL (1) | IL233819A0 (enExample) |
| IN (1) | IN2014DN05963A (enExample) |
| TW (1) | TWI596493B (enExample) |
| WO (1) | WO2013119770A1 (enExample) |
Families Citing this family (26)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| EP3862434A1 (en) * | 2013-11-04 | 2021-08-11 | Dow AgroSciences LLC | Optimal soybean loci |
| US10233465B2 (en) | 2013-11-04 | 2019-03-19 | Dow Agrosciences Llc | Optimal soybean loci |
| WO2015066638A2 (en) | 2013-11-04 | 2015-05-07 | Dow Agrosciences Llc | Optimal maize loci |
| BR102014027442B1 (pt) | 2013-11-04 | 2022-09-27 | Dow Agrosciences Llc | Molécula de ácido nucleico recombinante, uso de uma planta de milho, parte de planta de milho ou célula de planta de milho compreendendo a mesma e método para produzir uma célula vegetal transgênica compreendendo um dna de interesse |
| CN103824001A (zh) * | 2014-02-27 | 2014-05-28 | 北京诺禾致源生物信息科技有限公司 | 染色体的检测方法和装置 |
| US9600599B2 (en) * | 2014-05-13 | 2017-03-21 | Spiral Genetics, Inc. | Prefix burrows-wheeler transformation with fast operations on compressed data |
| TWI571763B (zh) * | 2014-12-01 | 2017-02-21 | 財團法人資訊工業策進會 | 次世代定序分析系統及其次世代定序分析方法 |
| US10006910B2 (en) | 2014-12-18 | 2018-06-26 | Agilome, Inc. | Chemically-sensitive field effect transistors, systems, and methods for manufacturing and using the same |
| EP3235010A4 (en) | 2014-12-18 | 2018-08-29 | Agilome, Inc. | Chemically-sensitive field effect transistor |
| US9859394B2 (en) | 2014-12-18 | 2018-01-02 | Agilome, Inc. | Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids |
| US9618474B2 (en) | 2014-12-18 | 2017-04-11 | Edico Genome, Inc. | Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids |
| US10020300B2 (en) | 2014-12-18 | 2018-07-10 | Agilome, Inc. | Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids |
| US9857328B2 (en) | 2014-12-18 | 2018-01-02 | Agilome, Inc. | Chemically-sensitive field effect transistors, systems and methods for manufacturing and using the same |
| SG11201707653TA (en) * | 2015-06-24 | 2017-10-30 | Samsung Life Public Welfare Foundation | Method and device for analyzing genes |
| WO2017083092A1 (en) * | 2015-11-10 | 2017-05-18 | Dow Agrosciences Llc | Methods and systems for predicting the risk of transgene silencing |
| TWI582631B (zh) * | 2015-11-20 | 2017-05-11 | 財團法人資訊工業策進會 | 用以分析細菌菌種之定序資料的系統及其方法 |
| WO2017101112A1 (zh) * | 2015-12-18 | 2017-06-22 | 云舟生物科技（广州）有限公司 | 载体设计方法及载体设计装置 |
| WO2017201081A1 (en) | 2016-05-16 | 2017-11-23 | Agilome, Inc. | Graphene fet devices, systems, and methods of using the same for sequencing nucleic acids |
| TWI629607B (zh) * | 2017-08-15 | 2018-07-11 | 極諾生技股份有限公司 | 建立腸道菌數據庫的方法和相關檢測系統 |
| US10649982B2 (en) * | 2017-11-09 | 2020-05-12 | Fry Laboratories, LLC | Automated database updating and curation |
| EP4082018A4 (en) * | 2019-12-23 | 2024-01-10 | Cold Spring Harbor Laboratory | Mixseq: mixture sequencing using compressed sensing for in-situ and in-vitro applications |
| KR102322308B1 (ko) | 2020-03-27 | 2021-11-05 | 주식회사 클리노믹스 | 일부 오믹스 정보를 활용하여 전체 오믹스 정보로 확대 생산하는 장치 및 방법 |
| CN111613272B (zh) * | 2020-05-21 | 2023-10-13 | 西湖大学 | 程序化框架gRNA及其应用 |
| CN113724783B (zh) * | 2021-06-16 | 2022-04-12 | 北京阅微基因技术股份有限公司 | 一种短串联重复序列重复数的检测和分型方法 |
| US12112792B2 (en) * | 2021-08-10 | 2024-10-08 | Micron Technology, Inc. | Memory device for wafer-on-wafer formed memory and logic |
| CN116343923B (zh) * | 2023-03-21 | 2023-12-08 | 哈尔滨工业大学 | 一种基因组结构变异同源性识别方法 |
Family Cites Families (8)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20030204317A1 (en) * | 2002-04-26 | 2003-10-30 | Affymetrix, Inc. | Methods, systems and software for displaying genomic sequence and annotations |
| JP2004139254A (ja) * | 2002-10-16 | 2004-05-13 | Nec Soft Ltd | 近傍遺伝子情報検索装置及び方法 |
| US20040241657A1 (en) * | 2003-05-28 | 2004-12-02 | Perlegen Sciences, Inc. | Liver related disease compositions and methods |
| GB2413796B (en) * | 2004-03-25 | 2006-03-29 | Global Genomics Ab | Methods and means for nucleic acid sequencing |
| CA2588243C (en) * | 2004-09-29 | 2013-06-11 | Pioneer Hi-Bred International, Inc. | Corn event das-59122-7 and methods for detection thereof |
| JP2006252541A (ja) * | 2005-02-10 | 2006-09-21 | Institute Of Physical & Chemical Research | アノテーション方法、アノテーションシステム、プログラムおよびコンピューター読み取り可能な記録媒体 |
| US8592211B2 (en) * | 2009-03-20 | 2013-11-26 | The Rockefeller University | Enhanced PiggyBac transposon and methods for transposon mutagenesis |
| EP2411537A2 (en) * | 2009-03-24 | 2012-02-01 | Yeda Research and Development Co. Ltd. | Methods of predicting pairability and secondary structures of rna molecules |
-
2013
- 2013-02-07 CN CN201380008411.9A patent/CN104272311B/zh not_active Expired - Fee Related
- 2013-02-07 AU AU2013217079A patent/AU2013217079B2/en not_active Ceased
- 2013-02-07 EP EP13746881.5A patent/EP2812831A4/en not_active Withdrawn
- 2013-02-07 WO PCT/US2013/025087 patent/WO2013119770A1/en not_active Ceased
- 2013-02-07 KR KR1020147021853A patent/KR20140119723A/ko not_active Ceased
- 2013-02-07 IN IN5963DEN2014 patent/IN2014DN05963A/en unknown
- 2013-02-07 BR BR112014019047A patent/BR112014019047A2/pt not_active Application Discontinuation
- 2013-02-07 AR ARP130100389A patent/AR089934A1/es not_active Application Discontinuation
- 2013-02-07 TW TW102104862A patent/TWI596493B/zh not_active IP Right Cessation
- 2013-02-07 CA CA2863524A patent/CA2863524A1/en not_active Abandoned
- 2013-02-07 JP JP2014556652A patent/JP6314091B2/ja active Active
- 2013-02-07 US US13/761,711 patent/US20130211729A1/en not_active Abandoned
-
2014
- 2014-07-27 IL IL233819A patent/IL233819A0/en unknown
Also Published As
| Publication number | Publication date |
|---|---|
| EP2812831A1 (en) | 2014-12-17 |
| IN2014DN05963A (enExample) | 2015-06-26 |
| AR089934A1 (es) | 2014-10-01 |
| BR112014019047A2 (pt) | 2017-06-27 |
| CN104272311A (zh) | 2015-01-07 |
| CN104272311B (zh) | 2018-08-28 |
| JP2015509623A (ja) | 2015-03-30 |
| AU2013217079B2 (en) | 2018-04-19 |
| AU2013217079A1 (en) | 2014-08-07 |
| TWI596493B (zh) | 2017-08-21 |
| IL233819A0 (en) | 2014-09-30 |
| TW201337618A (zh) | 2013-09-16 |
| HK1201951A1 (en) | 2015-09-11 |
| JP6314091B2 (ja) | 2018-04-18 |
| KR20140119723A (ko) | 2014-10-10 |
| US20130211729A1 (en) | 2013-08-15 |
| WO2013119770A1 (en) | 2013-08-15 |
| EP2812831A4 (en) | 2015-11-18 |
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Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| EEER | Examination request |
Effective date: 20180206 |
|
| FZDE | Discontinued |
Effective date: 20200207 |