GB2578709B - Context aware delta algorithm for genomic files - Google Patents

Context aware delta algorithm for genomic files Download PDF

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Publication number
GB2578709B
GB2578709B GB2003514.3A GB202003514A GB2578709B GB 2578709 B GB2578709 B GB 2578709B GB 202003514 A GB202003514 A GB 202003514A GB 2578709 B GB2578709 B GB 2578709B
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United Kingdom
Prior art keywords
context aware
delta algorithm
genomic
files
genomic files
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.)
Active
Application number
GB2003514.3A
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English (en)
Other versions
GB2578709A (en
GB202003514D0 (en
Inventor
Maharana Adyasha
Corneliu Constantinescu Mihail
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.)
International Business Machines Corp
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International Business Machines 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.)
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Publication date
Application filed by International Business Machines Corp filed Critical International Business Machines Corp
Publication of GB202003514D0 publication Critical patent/GB202003514D0/en
Publication of GB2578709A publication Critical patent/GB2578709A/en
Application granted granted Critical
Publication of GB2578709B publication Critical patent/GB2578709B/en
Active legal-status Critical Current
Anticipated expiration legal-status Critical

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Classifications

    • 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

Landscapes

  • 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)
GB2003514.3A 2017-08-31 2018-08-09 Context aware delta algorithm for genomic files Active GB2578709B (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
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)

Publication Number Publication Date
GB202003514D0 GB202003514D0 (en) 2020-04-29
GB2578709A GB2578709A (en) 2020-05-20
GB2578709B true GB2578709B (en) 2020-09-23

Family

ID=65435154

Family Applications (1)

Application Number Title Priority Date Filing Date
GB2003514.3A Active GB2578709B (en) 2017-08-31 2018-08-09 Context aware delta algorithm for genomic files

Country Status (5)

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

Families Citing this family (11)

* 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)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN103546160A (zh) * 2013-09-22 2014-01-29 上海交通大学 基于多参考序列的基因序列分级压缩方法
US8972201B2 (en) * 2011-12-24 2015-03-03 Tata Consultancy Services Limited Compression of genomic data file
US20160306919A1 (en) * 2013-12-06 2016-10-20 International Business Machines Corporation Genome compression and decompression

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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
WO2006052242A1 (en) * 2004-11-08 2006-05-18 Seirad, Inc. Methods and systems for compressing and comparing genomic data
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
US20110119240A1 (en) * 2009-11-18 2011-05-19 Dana Shapira Method and system for generating a bidirectional delta file
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
EP2595076B1 (en) * 2011-11-18 2019-05-15 Tata Consultancy Services Limited Compression of genomic data
US9715574B2 (en) * 2011-12-20 2017-07-25 Michael H. Baym Compressing, storing and searching sequence data
GB2507751A (en) * 2012-11-07 2014-05-14 Ibm Storing data files in a file system which provides reference data files
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
US8972201B2 (en) * 2011-12-24 2015-03-03 Tata Consultancy Services Limited Compression of genomic data file
CN103546160A (zh) * 2013-09-22 2014-01-29 上海交通大学 基于多参考序列的基因序列分级压缩方法
US20160306919A1 (en) * 2013-12-06 2016-10-20 International Business Machines Corporation Genome compression and decompression

Also Published As

Publication number Publication date
CN111095421A (zh) 2020-05-01
US20190065518A1 (en) 2019-02-28
JP2020533666A (ja) 2020-11-19
CN111095421B (zh) 2024-02-02
JP7157141B2 (ja) 2022-10-19
GB2578709A (en) 2020-05-20
GB202003514D0 (en) 2020-04-29
WO2019043481A1 (en) 2019-03-07
US11163726B2 (en) 2021-11-02

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Effective date: 20201123