CN114783523A - 使用分级反向索引表的dna比对 - Google Patents

使用分级反向索引表的dna比对 Download PDF

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CN114783523A
CN114783523A CN202210452629.4A CN202210452629A CN114783523A CN 114783523 A CN114783523 A CN 114783523A CN 202210452629 A CN202210452629 A CN 202210452629A CN 114783523 A CN114783523 A CN 114783523A
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M·B·多尔
J·D·加玛尼
S·V·伍德
D·G·阿拉斯塔斯
M·A·亨特
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Coherent Logix Inc
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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
    • 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
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/22—Indexing; Data structures therefor; Storage structures
    • G06F16/2228—Indexing structures
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/30—Information retrieval; Database structures therefor; File system structures therefor of unstructured textual data
    • G06F16/31—Indexing; Data structures therefor; Storage structures
    • G06F16/316—Indexing structures
    • G06F16/319—Inverted lists
    • 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
    • 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

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  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Databases & Information Systems (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Data Mining & Analysis (AREA)
  • Software Systems (AREA)
  • Bioethics (AREA)
  • General Physics & Mathematics (AREA)
  • General Engineering & Computer Science (AREA)
  • Artificial Intelligence (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
CN202210452629.4A 2015-10-21 2016-10-21 使用分级反向索引表的dna比对 Pending CN114783523A (zh)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US201562244541P 2015-10-21 2015-10-21
US62/244,541 2015-10-21
CN201680061446.2A CN108140071B (zh) 2015-10-21 2016-10-21 使用分级反向索引表的dna比对
PCT/US2016/058183 WO2017070514A1 (en) 2015-10-21 2016-10-21 Dna alignment using a hierarchical inverted index table

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EP (1) EP3365821B1 (enExample)
JP (1) JP6884143B2 (enExample)
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BR (1) BR112018007092B1 (enExample)
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US8705623B2 (en) * 2009-10-02 2014-04-22 Texas Instruments Incorporated Line-based compression for digital image data
US12125559B2 (en) * 2019-05-14 2024-10-22 Samsung Electronics Co., Ltd. Parallelizable sequence alignment systems and methods
CN112948446B (zh) * 2019-11-26 2024-08-16 北京京东振世信息技术有限公司 一种匹配产品单据的方法和装置
CN111402959A (zh) * 2020-03-13 2020-07-10 苏州浪潮智能科技有限公司 一种序列比对的方法、系统、设备及可读存储介质
IL281960B2 (en) 2021-04-01 2025-12-01 Zimmerman Israel System and method for rapid statistical pattern discovery
CN114329135B (zh) * 2021-12-08 2025-06-03 腾讯科技（深圳）有限公司 一种索引点离线排序方法、装置、设备及存储介质
CN116010427B (zh) * 2023-02-13 2025-11-14 长鑫存储技术有限公司 一种编号分配方法、装置、电子设备及存储介质

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US20040153255A1 (en) * 2003-02-03 2004-08-05 Ahn Tae-Jin Apparatus and method for encoding DNA sequence, and computer readable medium
US20120089338A1 (en) * 2009-03-13 2012-04-12 Life Technologies Corporation Computer implemented method for indexing reference genome
CN103336916A (zh) * 2013-07-05 2013-10-02 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
WO2014145503A2 (en) * 2013-03-15 2014-09-18 Lieber Institute For Brain Development Sequence alignment using divide and conquer maximum oligonucleotide mapping (dcmom), apparatus, system and method related thereto
CN104217134A (zh) * 2013-05-29 2014-12-17 诺布里斯股份有限公司 用于snp分析和基因组测序的系统和方法

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WO2005096208A1 (ja) * 2004-03-31 2005-10-13 Bio-Think Tank Co., Ltd. 塩基配列検索装置及び塩基配列検索方法
US7702640B1 (en) * 2005-12-29 2010-04-20 Amazon Technologies, Inc. Stratified unbalanced trees for indexing of data items within a computer system
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US20120089338A1 (en) * 2009-03-13 2012-04-12 Life Technologies Corporation Computer implemented method for indexing reference genome
WO2014145503A2 (en) * 2013-03-15 2014-09-18 Lieber Institute For Brain Development Sequence alignment using divide and conquer maximum oligonucleotide mapping (dcmom), apparatus, system and method related thereto
CN104217134A (zh) * 2013-05-29 2014-12-17 诺布里斯股份有限公司 用于snp分析和基因组测序的系统和方法
CN103336916A (zh) * 2013-07-05 2013-10-02 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

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EP3365821A1 (en) 2018-08-29
EP3365821B1 (en) 2022-06-29
JP2018535484A (ja) 2018-11-29
JP6884143B2 (ja) 2021-06-09
KR20180072684A (ko) 2018-06-29
US12087403B2 (en) 2024-09-10
US20250174304A1 (en) 2025-05-29
WO2017070514A1 (en) 2017-04-27
US20240203527A1 (en) 2024-06-20
CN108140071A (zh) 2018-06-08
US20170116370A1 (en) 2017-04-27
CN108140071B (zh) 2022-04-29
US11594301B2 (en) 2023-02-28
BR112018007092B1 (pt) 2024-02-20
EP3365821A4 (en) 2019-06-26
BR112018007092A2 (pt) 2018-10-23

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