JP6884143B2 - 階層的転置索引表を使用したｄｎａアラインメント - Google Patents

階層的転置索引表を使用したｄｎａアラインメント Download PDF

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JP6884143B2
JP6884143B2 JP2018520481A JP2018520481A JP6884143B2 JP 6884143 B2 JP6884143 B2 JP 6884143B2 JP 2018520481 A JP2018520481 A JP 2018520481A JP 2018520481 A JP2018520481 A JP 2018520481A JP 6884143 B2 JP6884143 B2 JP 6884143B2
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ドーア，マイケル・ビイ
ガーマニー，ジャン・ディ
ウッド，スティーヴン・ブイ
アラスタス，デーモン・ジイ
ハント，マーティン・エイ
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    • 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
    • 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
    • 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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  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
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JP2018520481A 2015-10-21 2016-10-21 階層的転置索引表を使用したｄｎａアラインメント Active JP6884143B2 (ja)

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US201562244541P 2015-10-21 2015-10-21
US62/244,541 2015-10-21
PCT/US2016/058183 WO2017070514A1 (en) 2015-10-21 2016-10-21 Dna alignment using a hierarchical inverted index table

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JP2018535484A JP2018535484A (ja) 2018-11-29
JP2018535484A5 JP2018535484A5 (enExample) 2019-09-05
JP6884143B2 true JP6884143B2 (ja) 2021-06-09

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US (3) US11594301B2 (enExample)
EP (1) EP3365821B1 (enExample)
JP (1) JP6884143B2 (enExample)
KR (1) KR20180072684A (enExample)
CN (2) CN114783523A (enExample)
BR (1) BR112018007092B1 (enExample)
WO (1) WO2017070514A1 (enExample)

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Publication number Priority date Publication date Assignee Title
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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Publication number Priority date Publication date Assignee Title
JPH08272824A (ja) * 1995-03-31 1996-10-18 Hitachi Software Eng Co Ltd 遺伝子配列データ自動検索方法
US20040153255A1 (en) * 2003-02-03 2004-08-05 Ahn Tae-Jin Apparatus and method for encoding DNA sequence, and computer readable medium
EP1732022A4 (en) * 2004-03-31 2008-09-24 Bio Think Tank Co Ltd APPARATUS FOR RECOVERING A BASIC SEQUENCE
US7702640B1 (en) * 2005-12-29 2010-04-20 Amazon Technologies, Inc. Stratified unbalanced trees for indexing of data items within a computer system
US8116988B2 (en) * 2006-05-19 2012-02-14 The University Of Chicago Method for indexing nucleic acid sequences for computer based searching
US8271206B2 (en) * 2008-04-21 2012-09-18 Softgenetics Llc DNA sequence assembly methods of short reads
WO2010104608A2 (en) * 2009-03-13 2010-09-16 Life Technologies Corporation Computer implemented method for indexing reference genome
CN101984445B (zh) * 2010-03-04 2012-03-14 深圳华大基因科技有限公司 一种基于聚合酶链式反应产物测序序列分型的实现方法和系统
US20140163900A1 (en) * 2012-06-02 2014-06-12 Whitehead Institute For Biomedical Research Analyzing short tandem repeats from high throughput sequencing data for genetic applications
US9679104B2 (en) * 2013-01-17 2017-06-13 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
US9792405B2 (en) * 2013-01-17 2017-10-17 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
US10381106B2 (en) * 2013-01-28 2019-08-13 Hasso-Plattner-Institut Fuer Softwaresystemtechnik Gmbh Efficient genomic read alignment in an in-memory database
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
US10191929B2 (en) * 2013-05-29 2019-01-29 Noblis, Inc. Systems and methods for SNP analysis and genome sequencing
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
NL2011817C2 (en) 2013-11-19 2015-05-26 Genalice B V A method of generating a reference index data structure and method for finding a position of a data pattern in a reference data structure.
WO2015127058A1 (en) * 2014-02-19 2015-08-27 Hospodor Andrew Efficient encoding and storage and retrieval of genomic data
NL2013120B1 (en) * 2014-07-03 2016-09-20 Genalice B V A method for finding associated positions of bases of a read on a reference genome.

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Publication number Publication date
BR112018007092A2 (pt) 2018-10-23
US11594301B2 (en) 2023-02-28
US20240203527A1 (en) 2024-06-20
BR112018007092B1 (pt) 2024-02-20
WO2017070514A1 (en) 2017-04-27
US20250174304A1 (en) 2025-05-29
US12087403B2 (en) 2024-09-10
EP3365821A4 (en) 2019-06-26
CN114783523A (zh) 2022-07-22
US20170116370A1 (en) 2017-04-27
EP3365821B1 (en) 2022-06-29
CN108140071A (zh) 2018-06-08
CN108140071B (zh) 2022-04-29
JP2018535484A (ja) 2018-11-29
EP3365821A1 (en) 2018-08-29
KR20180072684A (ko) 2018-06-29

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