CA3052824A1 - Procede et appareil pour la representation compacte de donnees bioinformatiques au moyen de plusieurs descripteurs genomiques - Google Patents
Procede et appareil pour la representation compacte de donnees bioinformatiques au moyen de plusieurs descripteurs genomiques Download PDFInfo
- Publication number
- CA3052824A1 CA3052824A1 CA3052824A CA3052824A CA3052824A1 CA 3052824 A1 CA3052824 A1 CA 3052824A1 CA 3052824 A CA3052824 A CA 3052824A CA 3052824 A CA3052824 A CA 3052824A CA 3052824 A1 CA3052824 A1 CA 3052824A1
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Links
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Classifications
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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
- G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
- G16B50/50—Compression of genetic data
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F3/00—Input arrangements for transferring data to be processed into a form capable of being handled by the computer; Output arrangements for transferring data from processing unit to output unit, e.g. interface arrangements
- G06F3/01—Input arrangements or combined input and output arrangements for interaction between user and computer
- G06F3/048—Interaction techniques based on graphical user interfaces [GUI]
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F7/00—Methods or arrangements for processing data by operating upon the order or content of the data handled
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F7/00—Methods or arrangements for processing data by operating upon the order or content of the data handled
- G06F7/58—Random or pseudo-random number generators
-
- 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
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
-
- 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
- G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
-
- 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
- G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
-
- 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
-
- 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
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- H—ELECTRICITY
- H04—ELECTRIC COMMUNICATION TECHNIQUE
- H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
- H04L9/00—Cryptographic mechanisms or cryptographic arrangements for secret or secure communications; Network security protocols
- H04L9/08—Key distribution or management, e.g. generation, sharing or updating, of cryptographic keys or passwords
- H04L9/0861—Generation of secret information including derivation or calculation of cryptographic keys or passwords
- H04L9/0866—Generation of secret information including derivation or calculation of cryptographic keys or passwords involving user or device identifiers, e.g. serial number, physical or biometrical information, DNA, hand-signature or measurable physical characteristics
-
- H—ELECTRICITY
- H04—ELECTRIC COMMUNICATION TECHNIQUE
- H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
- H04L9/00—Cryptographic mechanisms or cryptographic arrangements for secret or secure communications; Network security protocols
- H04L9/30—Public key, i.e. encryption algorithm being computationally infeasible to invert or user's encryption keys not requiring secrecy
- H04L9/3066—Public key, i.e. encryption algorithm being computationally infeasible to invert or user's encryption keys not requiring secrecy involving algebraic varieties, e.g. elliptic or hyper-elliptic curves
- H04L9/3073—Public key, i.e. encryption algorithm being computationally infeasible to invert or user's encryption keys not requiring secrecy involving algebraic varieties, e.g. elliptic or hyper-elliptic curves involving pairings, e.g. identity based encryption [IBE], bilinear mappings or bilinear pairings, e.g. Weil or Tate pairing
-
- H—ELECTRICITY
- H04—ELECTRIC COMMUNICATION TECHNIQUE
- H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
- H04L2209/00—Additional information or applications relating to cryptographic mechanisms or cryptographic arrangements for secret or secure communication H04L9/00
- H04L2209/30—Compression, e.g. Merkle-Damgard construction
-
- H—ELECTRICITY
- H04—ELECTRIC COMMUNICATION TECHNIQUE
- H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
- H04L2209/00—Additional information or applications relating to cryptographic mechanisms or cryptographic arrangements for secret or secure communication H04L9/00
- H04L2209/34—Encoding or coding, e.g. Huffman coding or error correction
-
- H—ELECTRICITY
- H04—ELECTRIC COMMUNICATION TECHNIQUE
- H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
- H04L2209/00—Additional information or applications relating to cryptographic mechanisms or cryptographic arrangements for secret or secure communication H04L9/00
- H04L2209/88—Medical equipments
Landscapes
- Engineering & Computer Science (AREA)
- Physics & Mathematics (AREA)
- Life Sciences & Earth Sciences (AREA)
- Theoretical Computer Science (AREA)
- Health & Medical Sciences (AREA)
- Medical Informatics (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Bioinformatics & Computational Biology (AREA)
- Biotechnology (AREA)
- Evolutionary Biology (AREA)
- General Health & Medical Sciences (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Biophysics (AREA)
- General Physics & Mathematics (AREA)
- Databases & Information Systems (AREA)
- Bioethics (AREA)
- General Engineering & Computer Science (AREA)
- Chemical & Material Sciences (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Analytical Chemistry (AREA)
- Data Mining & Analysis (AREA)
- Epidemiology (AREA)
- Public Health (AREA)
- Software Systems (AREA)
- Evolutionary Computation (AREA)
- Computer Vision & Pattern Recognition (AREA)
- Artificial Intelligence (AREA)
- Computer Security & Cryptography (AREA)
- Mathematical Analysis (AREA)
- Computer Networks & Wireless Communication (AREA)
- Mathematical Optimization (AREA)
- Pure & Applied Mathematics (AREA)
- Signal Processing (AREA)
- Genetics & Genomics (AREA)
- Computational Mathematics (AREA)
- Algebra (AREA)
- Human Computer Interaction (AREA)
- Mathematical Physics (AREA)
- Computing Systems (AREA)
- Molecular Biology (AREA)
Abstract
La présente invention concerne un procédé et un appareil destinés à la compression de données de séquences génomiques produites par des machines de séquençage du génome. Des lectures de séquences sont codées en les alignant par rapport à des séquences de référence préexistantes ou construites, le processus de codage étant composé d'une classification des lectures en classes de données suivie par le codage de chaque classe en termes d'une multiplicité de blocs de descripteurs. Des modèles de sources spécifiques et des codeurs d'entropie sont utilisés pour chaque classe de données dans laquelle les données sont divisées, et chaque bloc de descripteurs associé.
Applications Claiming Priority (5)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| PCT/US2017/017842 WO2018071055A1 (fr) | 2016-10-11 | 2017-02-14 | Procédé et appareil pour la représentation compacte de données bioinformatiques |
| USPCT/US2017/017842 | 2017-02-14 | ||
| PCT/US2017/041591 WO2018071080A2 (fr) | 2016-10-11 | 2017-07-11 | Procédé et systèmes pour la représentation et le traitement de données bio-informatiques à l'aide de séquences de référence |
| USPCT/US2017/041591 | 2017-07-11 | ||
| PCT/US2018/018092 WO2018152143A1 (fr) | 2017-02-14 | 2018-02-14 | Procédé et appareil pour la représentation compacte de données bioinformatiques au moyen de plusieurs descripteurs génomiques |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CA3052824A1 true CA3052824A1 (fr) | 2018-08-23 |
Family
ID=68609803
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA3052824A Pending CA3052824A1 (fr) | 2017-02-14 | 2018-02-14 | Procede et appareil pour la representation compacte de donnees bioinformatiques au moyen de plusieurs descripteurs genomiques |
Country Status (10)
| Country | Link |
|---|---|
| EP (1) | EP3583500A4 (fr) |
| KR (1) | KR20190113971A (fr) |
| AU (1) | AU2018221458B2 (fr) |
| CA (1) | CA3052824A1 (fr) |
| EA (1) | EA201991908A1 (fr) |
| IL (1) | IL268651A (fr) |
| MX (1) | MX2019009680A (fr) |
| SG (1) | SG11201907418YA (fr) |
| WO (1) | WO2018152143A1 (fr) |
| ZA (1) | ZA201905921B (fr) |
Families Citing this family (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN110189830B (zh) * | 2019-05-24 | 2021-06-08 | 杭州火树科技有限公司 | 基于机器学习的电子病历词库训练方法 |
| EP3896698A1 (fr) | 2020-04-15 | 2021-10-20 | Genomsys SA | Procédé et système pour la compression efficace des données en mpeg-g |
| KR102497634B1 (ko) * | 2020-12-21 | 2023-02-08 | 부산대학교 산학협력단 | 문자 빈도 기반 서열 재정렬을 통한 fastq 데이터 압축 방법 및 장치 |
Family Cites Families (7)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2002079391A2 (fr) * | 2001-04-02 | 2002-10-10 | Cytoprint, Inc. | Methode et appareil permettant de decouvrir, d'identifier et de comparer des mecanismes d'activite biologique |
| US7698067B2 (en) * | 2002-02-12 | 2010-04-13 | International Business Machines Corporation | Sequence pattern descriptors for transmembrane structural details |
| US7809765B2 (en) * | 2007-08-24 | 2010-10-05 | General Electric Company | Sequence identification and analysis |
| KR101922129B1 (ko) * | 2011-12-05 | 2018-11-26 | 삼성전자주식회사 | 차세대 시퀀싱을 이용하여 획득된 유전 정보를 압축 및 압축해제하는 방법 및 장치 |
| US9679104B2 (en) * | 2013-01-17 | 2017-06-13 | Edico Genome, Corp. | Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform |
| CN103336916B (zh) * | 2013-07-05 | 2016-04-06 | 中国科学院数学与系统科学研究院 | 一种测序序列映射方法及系统 |
| US10902937B2 (en) * | 2014-02-12 | 2021-01-26 | International Business Machines Corporation | Lossless compression of DNA sequences |
-
2018
- 2018-02-14 WO PCT/US2018/018092 patent/WO2018152143A1/fr unknown
- 2018-02-14 EP EP18753700.6A patent/EP3583500A4/fr active Pending
- 2018-02-14 MX MX2019009680A patent/MX2019009680A/es unknown
- 2018-02-14 EA EA201991908A patent/EA201991908A1/ru unknown
- 2018-02-14 KR KR1020197026877A patent/KR20190113971A/ko not_active Application Discontinuation
- 2018-02-14 CA CA3052824A patent/CA3052824A1/fr active Pending
- 2018-02-14 SG SG11201907418YA patent/SG11201907418YA/en unknown
- 2018-02-14 AU AU2018221458A patent/AU2018221458B2/en active Active
-
2019
- 2019-08-12 IL IL26865119A patent/IL268651A/en unknown
- 2019-09-09 ZA ZA2019/05921A patent/ZA201905921B/en unknown
Also Published As
| Publication number | Publication date |
|---|---|
| SG11201907418YA (en) | 2019-09-27 |
| AU2018221458A1 (en) | 2019-10-03 |
| KR20190113971A (ko) | 2019-10-08 |
| AU2018221458B2 (en) | 2022-12-08 |
| EP3583500A4 (fr) | 2020-12-16 |
| MX2019009680A (es) | 2019-10-09 |
| ZA201905921B (en) | 2021-05-26 |
| EA201991908A1 (ru) | 2020-01-21 |
| IL268651A (en) | 2019-10-31 |
| EP3583500A1 (fr) | 2019-12-25 |
| NZ757185A (en) | 2021-05-28 |
| WO2018152143A1 (fr) | 2018-08-23 |
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Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| EEER | Examination request |
Effective date: 20230214 |
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| EEER | Examination request |
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| EEER | Examination request |
Effective date: 20230214 |