JP7023711B2 - サンプル中の分類単位内の微生物の量を推定する方法及び装置 - Google Patents

サンプル中の分類単位内の微生物の量を推定する方法及び装置 Download PDF

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JP7023711B2
JP7023711B2 JP2017547118A JP2017547118A JP7023711B2 JP 7023711 B2 JP7023711 B2 JP 7023711B2 JP 2017547118 A JP2017547118 A JP 2017547118A JP 2017547118 A JP2017547118 A JP 2017547118A JP 7023711 B2 JP7023711 B2 JP 7023711B2
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sample
classification
microorganisms
species
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JP2018518725A (ja
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ヘンリー リン
シサーサン カマラカラン
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Koninklijke Philips NV
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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
    • 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
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • 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
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

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  • Life Sciences & Earth Sciences (AREA)
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  • Biotechnology (AREA)
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  • Spectroscopy & Molecular Physics (AREA)
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  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
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  • Databases & Information Systems (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Bioethics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
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JP2017547118A 2015-04-09 2016-04-08 サンプル中の分類単位内の微生物の量を推定する方法及び装置 Expired - Fee Related JP7023711B2 (ja)

Applications Claiming Priority (3)

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US201562145026P 2015-04-09 2015-04-09
US62/145,026 2015-04-09
PCT/EP2016/057799 WO2016162504A1 (en) 2015-04-09 2016-04-08 Method and apparatus for estimating the quantity of microorganisms within a taxonomic unit in a sample

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JP2018518725A JP2018518725A (ja) 2018-07-12
JP2018518725A5 JP2018518725A5 (enExample) 2019-03-22
JP7023711B2 true JP7023711B2 (ja) 2022-02-22

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US (1) US10998083B2 (enExample)
EP (1) EP3281136B1 (enExample)
JP (1) JP7023711B2 (enExample)
CN (1) CN107533587B (enExample)
AU (2) AU2016245213A1 (enExample)
BR (1) BR112017021318A2 (enExample)
CA (1) CA2981913A1 (enExample)
MX (1) MX391844B (enExample)
RU (1) RU2751241C2 (enExample)
WO (1) WO2016162504A1 (enExample)

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CA3054487A1 (en) * 2017-03-01 2018-09-07 Bluedot Llc Systems and methods for metagenomic analysis
CN110277139B (zh) * 2019-06-18 2023-03-21 江苏省产品质量监督检验研究院 一种基于互联网的微生物限度检查系统及方法
CN113284560B (zh) * 2021-04-28 2022-05-17 广州微远基因科技有限公司 病原检测背景微生物判断方法及应用
CN114334004B (zh) * 2021-12-04 2024-03-15 江苏先声医学诊断有限公司 一种病原微生物快速比对鉴定方法及其应用
CN115841847B (zh) * 2022-12-12 2023-05-12 哈尔滨因极科技有限公司 一种微生物信息测定及提取系统和方法

Family Cites Families (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6780602B2 (en) * 2001-11-01 2004-08-24 Microbiosystems, Limited Partnership Taxonomic identification of pathogenic microorganisms and their toxic proteins
CN102089419A (zh) * 2008-07-10 2011-06-08 塔康特精确有限公司 用于进行可培养细胞计数的方法、试剂盒和系统
EP2390810B1 (en) 2010-05-26 2019-10-16 Tata Consultancy Services Limited Taxonomic classification of metagenomic sequences
KR101347509B1 (ko) * 2011-06-20 2014-01-06 가톨릭대학교 산학협력단 섬망 고위험군 예측모형 시스템 및 그 예측모형 방법, 및 그것을 이용한 섬망 고위험군 예측 시스템
KR20160103175A (ko) * 2011-07-19 2016-08-31 오비지오 이미징 시스템스 엔.브이. 세포 샘플에서의 암 세포들의 검출 및/또는 분류를 위한 방법 및 시스템
US9914979B2 (en) * 2013-03-04 2018-03-13 Fry Laboratories, LLC Method and kit for characterizing microorganisms
CN104252627A (zh) * 2013-06-28 2014-12-31 广州华多网络科技有限公司 Svm分类器训练样本获取方法、训练方法及其系统
CN103627800B (zh) * 2013-11-14 2015-02-25 浙江天科高新技术发展有限公司 环境微生物快速检测方法

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
Adam L Bazinet 他１名，A comparative evaluation of sequence classification programs，BMC Bioinformatics，BioMed Central，2012年05月10日，volume 13, Article number: 92，検索日：令和２年４月１０日，ＵＲＬ：https://doi.org/10.1186/1471-2105-13-92
Derrick E Wood 他１名，Kraken: ultrafast metagenomic sequence classification using exact alignments，Genome Biology，BioMed Central，2014年03月03日，volume 15, Article number: R46，検索日：令和２年４月１０日，ＵＲＬ：https://doi.org/10.1186/gb-2014-15-3-r46
Rogan Carr 他２名，Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution，PLOS Computational Biology，Public Library of Science，2013年10月17日，Vol.9，pp.1-15，検索日：令和２年４月１０日，ＵＲＬ：https://doi.org/10.1371/journal.pcbi.1003292

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US10998083B2 (en) 2021-05-04
AU2021212155B2 (en) 2023-06-29
AU2016245213A1 (en) 2017-11-23
BR112017021318A2 (pt) 2018-06-26
US20180129777A1 (en) 2018-05-10
JP2018518725A (ja) 2018-07-12
RU2751241C2 (ru) 2021-07-12
CA2981913A1 (en) 2016-10-13
MX2017012758A (es) 2018-01-30
CN107533587B (zh) 2021-10-08
MX391844B (es) 2025-03-21
WO2016162504A1 (en) 2016-10-13
RU2017138867A3 (enExample) 2020-06-26
RU2017138867A (ru) 2019-05-13
EP3281136A1 (en) 2018-02-14
EP3281136B1 (en) 2024-06-05
CN107533587A (zh) 2018-01-02
AU2021212155A1 (en) 2021-08-26

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