SG11201903269QA - Method and apparatus for the access to bioinformatics data structured in access units - Google Patents

Method and apparatus for the access to bioinformatics data structured in access units

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Publication number
SG11201903269QA
SG11201903269QA SG11201903269QA SG11201903269QA SG11201903269QA SG 11201903269Q A SG11201903269Q A SG 11201903269QA SG 11201903269Q A SG11201903269Q A SG 11201903269QA SG 11201903269Q A SG11201903269Q A SG 11201903269QA SG 11201903269Q A SG11201903269Q A SG 11201903269QA
Authority
SG
Singapore
Prior art keywords
pct
access
international
october
data
Prior art date
Application number
SG11201903269QA
Inventor
Claudio Alberti
Giorgio Zoia
Daniele Renzi
Mohamed Baluch
Original Assignee
Genomsys Sa
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.)
Filing date
Publication date
Priority claimed from PCT/EP2016/074307 external-priority patent/WO2018068829A1/en
Priority claimed from PCT/EP2016/074311 external-priority patent/WO2018068830A1/en
Priority claimed from PCT/EP2016/074301 external-priority patent/WO2018068828A1/en
Priority claimed from PCT/EP2016/074297 external-priority patent/WO2018068827A1/en
Application filed by Genomsys Sa filed Critical Genomsys Sa
Priority claimed from PCT/US2017/041579 external-priority patent/WO2018071078A1/en
Publication of SG11201903269QA publication Critical patent/SG11201903269QA/en

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Classifications

    • 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
    • G16B50/50—Compression of genetic data
    • 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
    • H03M7/3084—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction using adaptive string matching, e.g. the Lempel-Ziv method
    • H03M7/3086—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction using adaptive string matching, e.g. the Lempel-Ziv method employing a sliding window, e.g. LZ77
    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F21/00—Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
    • G06F21/10—Protecting distributed programs or content, e.g. vending or licensing of copyrighted material ; Digital rights management [DRM]
    • G06F21/12—Protecting executable software
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F21/00—Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
    • G06F21/60—Protecting data
    • G06F21/62—Protecting access to data via a platform, e.g. using keys or access control rules
    • G06F21/6218—Protecting access to data via a platform, e.g. using keys or access control rules to a system of files or objects, e.g. local or distributed file system or database
    • G06F21/6245—Protecting personal data, e.g. for financial or medical purposes
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20—Sequence assembly
    • 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
    • G16B40/10—Signal processing, e.g. from mass spectrometry [MS] or from PCR
    • 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
    • G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
    • 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
    • G16B50/20—Heterogeneous data integration
    • 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
    • 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
    • H03M7/3084—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction using adaptive string matching, e.g. the Lempel-Ziv method
    • H03M7/3088—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction using adaptive string matching, e.g. the Lempel-Ziv method employing the use of a dictionary, e.g. LZ78
    • 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
    • H03M7/3084—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction using adaptive string matching, e.g. the Lempel-Ziv method
    • H03M7/3091—Data deduplication
    • 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
    • H03M7/3084—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction using adaptive string matching, e.g. the Lempel-Ziv method
    • H03M7/3091—Data deduplication
    • H03M7/3095—Data deduplication using variable length segments
    • 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
    • H03M7/40—Conversion to or from variable length codes, e.g. Shannon-Fano code, Huffman code, Morse code
    • 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
    • H03M7/60—General implementation details not specific to a particular type of compression
    • H03M7/6005—Decoder aspects
    • 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
    • H03M7/70—Type of the data to be coded, other than image and sound

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Bioethics (AREA)
  • Chemical & Material Sciences (AREA)
  • Databases & Information Systems (AREA)
  • Software Systems (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • General Physics & Mathematics (AREA)
  • Computer Hardware Design (AREA)
  • Computer Security & Cryptography (AREA)
  • Genetics & Genomics (AREA)
  • Data Mining & Analysis (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Technology Law (AREA)
  • Multimedia (AREA)
  • Zoology (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Evolutionary Computation (AREA)
  • Immunology (AREA)
  • Signal Processing (AREA)
  • Artificial Intelligence (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Epidemiology (AREA)
  • Microbiology (AREA)
  • Public Health (AREA)

Abstract

PUBLISHEDUNDER THE PATENT COOPERATION TREATY (PCT) () INTERNATIONAL APPLICATION (19) World Intellectual Property Organization International Bureau (43) International Publication Date Iiiimmomiolollmonoloolomoionitiomovoimill (10) International Publication Number WO 2018/071078 Al 0 CC mode %anomie Region Aft Cies 1 M F.11 ,M AURJA 1 t•Uk). AUS.„1 19 April 2018 (19.04.2018) WIPO I PCT (51) International Patent Classification: 11 October 2016 (11.10.2016) EP GO6F 19/18 (2011.01) GO6F 21/12 (2013.01) PCT/EP2016/74301 GOOF 19/20 (2011.01) HO3M 7/30 (2006.01) 11 October 2016 (11.10.2016) EP GOOF 19/22 (2011.01) PCT/EP2017/017842 (21) International Application Number: 14 February 2017 (14.02.2017) PCT/EP2017/017841 US PCT/US2017/041579 14 February 2017 (14.02.2017) US (22) International Filing Date: (71) Applicant: GENOMSYS SA; Chemin De La Raye 13, 11 July 2017 (11.07.2017) 1024 Ecublens Vd (CH). (25) Filing Language: English (72) Inventor; and (26) Publication Language: English (71) Applicant: BALUCH, Mohamed, Khoso [US/US]; 4439 Woodsedge Ct, Chantilly, VA 20151 (US). (30) Priority Data: PCT/EP2016/074307 (72) Inventors: ALBERTI, Claudio; Chemin Des Esserts 1, 11 October 2016 (11.10.2016) EP PCT/EP2016/074297 11 October 2016 (11.10.2016) EP PCT/EP2016/074311 1213 Petit-lancy (CH). ZOIA, Giorgio; Chemin Des Croix- rouges 10, 1007 Lausanne (CH). RENZI, Daniele; Route Aloys-fauquez 105, 1018 Lausanne (CH). (54) Title: METHOD AND APPARATUS FOR THE ACCESS TO BIOINFORMATICS DATA STRUCTURED IN ACCESS UNITS GRC mode AUO_CI AtiiO Region 1 Figure 17 (57) : Method and apparatus for the coding and selective access of compressed genomic sequence data produced by genomic sequencing machines. The coding process is based on aligning sequence reads with respect to pre-existing or constructed reference sequences, on classifying and coding the sequence reads by means of sets of descriptors, and further partitioning the descriptor sets into access units of different types. Efficient selective access to specific genomic regions with the guarantee of retrieving all sequence reads mapped to those regions, is provided by: signaling the type of data mapping configuration used to store or transmit the descriptor sets, determining the minimum number of access units that need to be retrieved and decoded to access a genomic region, providing a master index table that contain all information for optimizing the data access process. [Continued on next page] GC N O N O GC O O WO 2018/071078 Al MIDEDIMOMOIDEIREEMONOMOIONMEMOVOIS (74) Agent: BILICKI, Byron et al.; The Bilicki Law Finn, P.C., 1285 North Main Street, Jamestown, NY 14701 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Declarations under Rule 4.17: — as to the identity of the inventor (Rule 4.17(0) Published: — with international search report (Art. 21(3))
SG11201903269QA 2016-10-11 2017-07-11 Method and apparatus for the access to bioinformatics data structured in access units SG11201903269QA (en)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
PCT/EP2016/074307 WO2018068829A1 (en) 2016-10-11 2016-10-11 Method and apparatus for compact representation of bioinformatics data
PCT/EP2016/074311 WO2018068830A1 (en) 2016-10-11 2016-10-11 Method and system for the transmission of bioinformatics data
PCT/EP2016/074301 WO2018068828A1 (en) 2016-10-11 2016-10-11 Method and system for storing and accessing bioinformatics data
PCT/EP2016/074297 WO2018068827A1 (en) 2016-10-11 2016-10-11 Efficient data structures for bioinformatics information representation
EP2017017841 2017-02-14
EP2017017842 2017-02-14
PCT/US2017/041579 WO2018071078A1 (en) 2016-10-11 2017-07-11 Method and apparatus for the access to bioinformatics data structured in access units

Publications (1)

Publication Number Publication Date
SG11201903269QA true SG11201903269QA (en) 2019-05-30

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SG11201903269QA SG11201903269QA (en) 2016-10-11 2017-07-11 Method and apparatus for the access to bioinformatics data structured in access units
SG11201907415SA SG11201907415SA (en) 2016-10-11 2017-12-14 Method and systems for the reconstruction of genomic reference sequences from compressed genomic sequence reads

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SG11201907415SA SG11201907415SA (en) 2016-10-11 2017-12-14 Method and systems for the reconstruction of genomic reference sequences from compressed genomic sequence reads

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EP (1) EP3583249B1 (en)
KR (2) KR102421458B1 (en)
AU (2) AU2017342754A1 (en)
CA (2) CA3040057A1 (en)
CL (1) CL2019000971A1 (en)
CO (1) CO2019009919A2 (en)
IL (3) IL268649B1 (en)
MX (3) MX2019004129A (en)
PH (1) PH12019501880A1 (en)
SG (2) SG11201903269QA (en)
WO (1) WO2018151786A1 (en)

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US20200058379A1 (en) * 2018-08-20 2020-02-20 The Board Of Trustees Of The Leland Stanford Junior University Systems and Methods for Compressing Genetic Sequencing Data and Uses Thereof
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CN111326216B (en) * 2020-02-27 2023-07-21 中国科学院计算技术研究所 Rapid partitioning method for big data gene sequencing file
KR102497634B1 (en) * 2020-12-21 2023-02-08 부산대학교 산학협력단 Method and apparatus for compressing fastq data through character frequency-based sequence reordering

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EP3583249A4 (en) 2020-12-02
CO2019009919A2 (en) 2019-12-10
US20200043570A1 (en) 2020-02-06
WO2018151786A1 (en) 2018-08-23
PH12019501880A1 (en) 2020-06-29
EP3583249A1 (en) 2019-12-25
AU2017398951A1 (en) 2019-10-10
MX2019004131A (en) 2020-01-30
MX2019004129A (en) 2019-08-29
CA3040057A1 (en) 2018-04-19
IL268649B1 (en) 2024-03-01
KR20190062551A (en) 2019-06-05
KR20190113969A (en) 2019-10-08
SG11201907415SA (en) 2019-09-27
IL268650B1 (en) 2024-03-01
CA3052773A1 (en) 2018-08-23
US11763918B2 (en) 2023-09-19
AU2017342754A1 (en) 2019-05-02
KR102421458B1 (en) 2022-07-14
EP3583249B1 (en) 2023-07-19
CL2019000971A1 (en) 2019-08-23
IL268650A (en) 2019-10-31
MX2019009682A (en) 2019-10-09
IL268649A (en) 2019-10-31
IL265956A (en) 2019-05-30

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