JP7157141B2 - ゲノム・ファイルのためのコンテキスト・アウェア差分アルゴリズム - Google Patents

ゲノム・ファイルのためのコンテキスト・アウェア差分アルゴリズム Download PDF

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JP7157141B2
JP7157141B2 JP2020509515A JP2020509515A JP7157141B2 JP 7157141 B2 JP7157141 B2 JP 7157141B2 JP 2020509515 A JP2020509515 A JP 2020509515A JP 2020509515 A JP2020509515 A JP 2020509515A JP 7157141 B2 JP7157141 B2 JP 7157141B2
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file
genome
files
source
based differential
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Japanese (ja)
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JP2020533666A (ja
JP2020533666A5 (https=
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マハラナ、アジャシャ
コンスタンチネスキュ、ミハイル、コルネリウ
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International Business Machines Corp
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International Business Machines Corp
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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
    • G06F16/10—File systems; File servers
    • G06F16/17—Details of further file system functions
    • G06F16/174—Redundancy elimination performed by the file system
    • G06F16/1744—Redundancy elimination performed by the file system using compression, e.g. sparse files
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
    • H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
    • H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction

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  • Engineering & Computer Science (AREA)
  • Theoretical Computer Science (AREA)
  • Data Mining & Analysis (AREA)
  • Databases & Information Systems (AREA)
  • Physics & Mathematics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Physics & Mathematics (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
  • Compression, Expansion, Code Conversion, And Decoders (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
JP2020509515A 2017-08-31 2018-08-09 ゲノム・ファイルのためのコンテキスト・アウェア差分アルゴリズム Active JP7157141B2 (ja)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US15/693,019 2017-08-31
US15/693,019 US11163726B2 (en) 2017-08-31 2017-08-31 Context aware delta algorithm for genomic files
PCT/IB2018/056009 WO2019043481A1 (en) 2017-08-31 2018-08-09 DELTA ALGORITHM SENSITIVE TO THE CONTEXT FOR GENOMIC FILES

Publications (3)

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JP2020533666A JP2020533666A (ja) 2020-11-19
JP2020533666A5 JP2020533666A5 (https=) 2021-02-12
JP7157141B2 true JP7157141B2 (ja) 2022-10-19

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JP2020509515A Active JP7157141B2 (ja) 2017-08-31 2018-08-09 ゲノム・ファイルのためのコンテキスト・アウェア差分アルゴリズム

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US (1) US11163726B2 (https=)
JP (1) JP7157141B2 (https=)
CN (1) CN111095421B (https=)
GB (1) GB2578709B (https=)
WO (1) WO2019043481A1 (https=)

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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10554220B1 (en) * 2019-01-30 2020-02-04 International Business Machines Corporation Managing compression and storage of genomic data
US11188503B2 (en) * 2020-02-18 2021-11-30 International Business Machines Corporation Record-based matching in data compression
CN113012755B (zh) * 2021-04-12 2023-10-27 聊城大学 基因组atcg的检索方法
US12580047B2 (en) 2022-01-18 2026-03-17 Dell Products L.P. Biological sequence compression using sequence alignment
US12530320B2 (en) 2022-01-18 2026-01-20 Dell Products L.P. File compression using sequence splits and sequence alignment
US12572509B2 (en) 2022-01-18 2026-03-10 Dell Products L.P. Structure based file compression using sequence alignment
US12511260B2 (en) * 2022-01-18 2025-12-30 Dell Products L.P. File compression using sequence alignment
US12353358B2 (en) 2022-01-18 2025-07-08 Dell Products L.P. Adding content to compressed files using sequence alignment
US12339811B2 (en) 2022-04-12 2025-06-24 Dell Products L.P. Compressing multiple dimension files using sequence alignment
US11977517B2 (en) 2022-04-12 2024-05-07 Dell Products L.P. Warm start file compression using sequence alignment
US12216621B2 (en) * 2022-04-12 2025-02-04 Dell Products L.P. Hyperparameter optimization in file compression using sequence alignment

Citations (3)

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Publication number Priority date Publication date Assignee Title
US20080077607A1 (en) 2004-11-08 2008-03-27 Seirad Inc. Methods and Systems for Compressing and Comparing Genomic Data
US20110119240A1 (en) 2009-11-18 2011-05-19 Dana Shapira Method and system for generating a bidirectional delta file
US20130132353A1 (en) 2011-11-18 2013-05-23 Tata Consultancy Services Limited Compression Of Genomic Data

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US20040086861A1 (en) * 2000-04-19 2004-05-06 Satoshi Omori Method and device for recording sequence information on nucleotides and amino acids
CN1680589A (zh) * 2003-06-06 2005-10-12 李志广 基因芯片用人类白细胞抗原分型探针的筛选及其应用方法
US7657383B2 (en) * 2004-05-28 2010-02-02 International Business Machines Corporation Method, system, and apparatus for compactly storing a subject genome
CN101535945A (zh) * 2006-04-25 2009-09-16 英孚威尔公司 全文查询和搜索系统及其使用方法
WO2011106629A2 (en) 2010-02-26 2011-09-01 Life Technologies Corporation Modified proteins and methods of making and using same
WO2012092515A2 (en) 2010-12-30 2012-07-05 Life Technologies Corporation Methods, systems, and computer readable media for nucleic acid sequencing
US9715574B2 (en) * 2011-12-20 2017-07-25 Michael H. Baym Compressing, storing and searching sequence data
EP2608096B1 (en) 2011-12-24 2020-08-05 Tata Consultancy Services Ltd. Compression of genomic data file
GB2507751A (en) * 2012-11-07 2014-05-14 Ibm Storing data files in a file system which provides reference data files
CN103546160B (zh) 2013-09-22 2016-07-06 上海交通大学 基于多参考序列的基因序列分级压缩方法
CN104699998A (zh) 2013-12-06 2015-06-10 国际商业机器公司 用于对基因组进行压缩和解压缩的方法和装置
NL2012222C2 (en) * 2014-02-06 2015-08-10 Genalice B V A method of storing/reconstructing a multitude of sequences in/from a data storage structure.
GB2530012A (en) * 2014-08-05 2016-03-16 Illumina Cambridge Ltd Methods and systems for data analysis and compression

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20080077607A1 (en) 2004-11-08 2008-03-27 Seirad Inc. Methods and Systems for Compressing and Comparing Genomic Data
US20110119240A1 (en) 2009-11-18 2011-05-19 Dana Shapira Method and system for generating a bidirectional delta file
US20130132353A1 (en) 2011-11-18 2013-05-23 Tata Consultancy Services Limited Compression Of Genomic Data

Also Published As

Publication number Publication date
CN111095421A (zh) 2020-05-01
US20190065518A1 (en) 2019-02-28
JP2020533666A (ja) 2020-11-19
GB2578709B (en) 2020-09-23
CN111095421B (zh) 2024-02-02
GB2578709A (en) 2020-05-20
GB202003514D0 (en) 2020-04-29
WO2019043481A1 (en) 2019-03-07
US11163726B2 (en) 2021-11-02

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