EP3317440A4 - Systèmes, appareils et procédés bioinformatiques exécutés sur une plate-forme de traitement à circuit intégré - Google Patents

Systèmes, appareils et procédés bioinformatiques exécutés sur une plate-forme de traitement à circuit intégré Download PDF

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Publication number
EP3317440A4
EP3317440A4 EP16818934.8A EP16818934A EP3317440A4 EP 3317440 A4 EP3317440 A4 EP 3317440A4 EP 16818934 A EP16818934 A EP 16818934A EP 3317440 A4 EP3317440 A4 EP 3317440A4
Authority
EP
European Patent Office
Prior art keywords
apparatuses
integrated circuit
processing platform
circuit processing
methods executed
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.)
Withdrawn
Application number
EP16818934.8A
Other languages
German (de)
English (en)
Other versions
EP3317440A1 (fr
Inventor
Pieter Van Rooyen
Michael Ruehle
Rami Mehio
Mark Hahm
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Edico Genome Corp
Original Assignee
Edico Genome 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
Priority claimed from US14/811,836 external-priority patent/US20220019919A1/en
Priority claimed from US15/048,935 external-priority patent/US20160171153A1/en
Priority claimed from US15/059,221 external-priority patent/US10068054B2/en
Priority claimed from US15/094,939 external-priority patent/US9792405B2/en
Application filed by Edico Genome Corp filed Critical Edico Genome Corp
Priority to EP19199685.9A priority Critical patent/EP3608913A1/fr
Publication of EP3317440A1 publication Critical patent/EP3317440A1/fr
Publication of EP3317440A4 publication Critical patent/EP3317440A4/fr
Withdrawn legal-status Critical Current

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
    • 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
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search

Landscapes

  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Theoretical Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
EP16818934.8A 2015-07-02 2016-07-01 Systèmes, appareils et procédés bioinformatiques exécutés sur une plate-forme de traitement à circuit intégré Withdrawn EP3317440A4 (fr)

Priority Applications (1)

Application Number Priority Date Filing Date Title
EP19199685.9A EP3608913A1 (fr) 2015-07-02 2016-07-01 Systèmes, appareils et procédés bioinformatiques exécutés sur une plate-forme de traitement à circuit intégré

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US201562188443P 2015-07-02 2015-07-02
US14/811,836 US20220019919A1 (en) 2015-07-02 2015-07-29 Method And System For A Reduced Computation Hidden Markov Model In Computational Biology Applications
US15/048,935 US20160171153A1 (en) 2013-01-17 2016-02-19 Bioinformatics Systems, Apparatuses, And Methods Executed On An Integrated Circuit Processing Platform
US15/059,221 US10068054B2 (en) 2013-01-17 2016-03-02 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
US15/094,939 US9792405B2 (en) 2013-01-17 2016-04-08 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
PCT/US2016/040842 WO2017004589A1 (fr) 2015-07-02 2016-07-01 Systèmes, appareils et procédés bioinformatiques exécutés sur une plate-forme de traitement à circuit intégré

Related Child Applications (1)

Application Number Title Priority Date Filing Date
EP19199685.9A Division EP3608913A1 (fr) 2015-07-02 2016-07-01 Systèmes, appareils et procédés bioinformatiques exécutés sur une plate-forme de traitement à circuit intégré

Publications (2)

Publication Number Publication Date
EP3317440A1 EP3317440A1 (fr) 2018-05-09
EP3317440A4 true EP3317440A4 (fr) 2019-03-27

Family

ID=57609574

Family Applications (2)

Application Number Title Priority Date Filing Date
EP16818934.8A Withdrawn EP3317440A4 (fr) 2015-07-02 2016-07-01 Systèmes, appareils et procédés bioinformatiques exécutés sur une plate-forme de traitement à circuit intégré
EP19199685.9A Pending EP3608913A1 (fr) 2015-07-02 2016-07-01 Systèmes, appareils et procédés bioinformatiques exécutés sur une plate-forme de traitement à circuit intégré

Family Applications After (1)

Application Number Title Priority Date Filing Date
EP19199685.9A Pending EP3608913A1 (fr) 2015-07-02 2016-07-01 Systèmes, appareils et procédés bioinformatiques exécutés sur une plate-forme de traitement à circuit intégré

Country Status (4)

Country Link
EP (2) EP3317440A4 (fr)
AU (3) AU2016287752B2 (fr)
HK (1) HK1254581A1 (fr)
WO (1) WO2017004589A1 (fr)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US12431218B2 (en) 2022-03-08 2025-09-30 Illumina, Inc. Multi-pass software-accelerated genomic read mapping engine

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11183270B2 (en) 2017-12-07 2021-11-23 International Business Machines Corporation Next generation sequencing sorting in time and space complexity using location integers
JP7562426B2 (ja) 2018-10-31 2024-10-07 イルミナ インコーポレイテッド 配列決定リードのグルーピングおよびコラプシングのためのシステムおよび方法
MX2020014030A (es) * 2019-05-24 2021-03-09 Illumina Inc Extensión flexible de seed para mapeo genómico de tabla hash.
CN111416654B (zh) * 2020-03-16 2021-07-09 北京邮电大学 一种基于硬件加速的卫星虚拟化信关站传输架构
CN111370064B (zh) * 2020-03-19 2023-05-05 山东大学 基于simd的哈希函数的基因序列快速分类方法及系统
US12367284B2 (en) * 2020-07-20 2025-07-22 Cybereason Inc. Systems and methods for determining measurements of similarity between various types of data
US20230212666A1 (en) * 2021-12-30 2023-07-06 Seagate Technology Llc Segmentation and labeling for single molecule sequencing
WO2025221988A1 (fr) * 2024-04-17 2025-10-23 Roche Sequencing Solutions, Inc. Systèmes et procédés d'appel de petits variants somatiques

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20140371110A1 (en) * 2013-01-17 2014-12-18 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US701100A (en) * 1901-05-16 1902-05-27 Samuel Stewart Gas heating-stove.
KR101188886B1 (ko) * 2010-10-22 2012-10-09 삼성에스디에스 주식회사 유전 정보 관리 시스템 및 방법
US9600625B2 (en) * 2012-04-23 2017-03-21 Bina Technologies, Inc. Systems and methods for processing nucleic acid sequence data
GB2523495A (en) 2013-01-17 2015-08-26 Edico Genome Corp Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
US9734284B2 (en) * 2013-03-15 2017-08-15 Micron Technology, Inc. Hardware acceleration of short read mapping for genomic and other types of analyses

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20140371110A1 (en) * 2013-01-17 2014-12-18 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US12431218B2 (en) 2022-03-08 2025-09-30 Illumina, Inc. Multi-pass software-accelerated genomic read mapping engine

Also Published As

Publication number Publication date
EP3608913A1 (fr) 2020-02-12
WO2017004589A1 (fr) 2017-01-05
AU2016287752A1 (en) 2018-02-22
HK1254581A1 (zh) 2019-07-19
AU2024201692A1 (en) 2024-05-02
EP3317440A1 (fr) 2018-05-09
AU2016287752B2 (en) 2021-12-02
AU2022201429A1 (en) 2022-03-24

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