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EP3583500A4 - METHOD AND DEVICE FOR COMPACT REPRESENTATION OF BIOINFORMATICS DATA USING SEVERAL GENOMIC DESCRIPTORS - Google Patents

METHOD AND DEVICE FOR COMPACT REPRESENTATION OF BIOINFORMATICS DATA USING SEVERAL GENOMIC DESCRIPTORS Download PDF

Info

Publication number
EP3583500A4
EP3583500A4 EP18753700.6A EP18753700A EP3583500A4 EP 3583500 A4 EP3583500 A4 EP 3583500A4 EP 18753700 A EP18753700 A EP 18753700A EP 3583500 A4 EP3583500 A4 EP 3583500A4
Authority
EP
European Patent Office
Prior art keywords
compact representation
bioinformatics data
several genomic
genomic descriptors
descriptors
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.)
Pending
Application number
EP18753700.6A
Other languages
German (de)
French (fr)
Other versions
EP3583500A1 (en
Inventor
Mohamed Khoso BALUCH
Claudio ALBERTI
Giorgio Zoia
Daniele RENZI
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.)
Koninklijke Philips NV
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/US2017/017842 external-priority patent/WO2018071055A1/en
Application filed by Genomsys SA filed Critical Genomsys SA
Publication of EP3583500A1 publication Critical patent/EP3583500A1/en
Publication of EP3583500A4 publication Critical patent/EP3583500A4/en
Pending legal-status Critical Current

Links

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
    • 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
    • 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
    • G16B50/50—Compression of genetic data
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F3/00—Input arrangements for transferring data to be processed into a form capable of being handled by the computer; Output arrangements for transferring data from processing unit to output unit, e.g. interface arrangements
    • G06F3/01—Input arrangements or combined input and output arrangements for interaction between user and computer
    • G06F3/048—Interaction techniques based on graphical user interfaces [GUI]
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F7/00—Methods or arrangements for processing data by operating upon the order or content of the data handled
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F7/00—Methods or arrangements for processing data by operating upon the order or content of the data handled
    • G06F7/58—Random or pseudo-random number generators
    • 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
    • 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
    • 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
    • G16B50/10—Ontologies; Annotations
    • 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
    • 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
    • G16B99/00—Subject matter not provided for in other groups of this subclass
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
    • H04L9/00—Cryptographic mechanisms or cryptographic arrangements for secret or secure communications; Network security protocols
    • H04L9/08—Key distribution or management, e.g. generation, sharing or updating, of cryptographic keys or passwords
    • H04L9/0861—Generation of secret information including derivation or calculation of cryptographic keys or passwords
    • H04L9/0866—Generation of secret information including derivation or calculation of cryptographic keys or passwords involving user or device identifiers, e.g. serial number, physical or biometrical information, DNA, hand-signature or measurable physical characteristics
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
    • H04L9/00—Cryptographic mechanisms or cryptographic arrangements for secret or secure communications; Network security protocols
    • H04L9/30—Public key, i.e. encryption algorithm being computationally infeasible to invert or user's encryption keys not requiring secrecy
    • H04L9/3066—Public key, i.e. encryption algorithm being computationally infeasible to invert or user's encryption keys not requiring secrecy involving algebraic varieties, e.g. elliptic or hyper-elliptic curves
    • H04L9/3073—Public key, i.e. encryption algorithm being computationally infeasible to invert or user's encryption keys not requiring secrecy involving algebraic varieties, e.g. elliptic or hyper-elliptic curves involving pairings, e.g. identity based encryption [IBE], bilinear mappings or bilinear pairings, e.g. Weil or Tate pairing
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
    • H04L2209/00—Additional information or applications relating to cryptographic mechanisms or cryptographic arrangements for secret or secure communication H04L9/00
    • H04L2209/30—Compression, e.g. Merkle-Damgard construction
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
    • H04L2209/00—Additional information or applications relating to cryptographic mechanisms or cryptographic arrangements for secret or secure communication H04L9/00
    • H04L2209/34—Encoding or coding, e.g. Huffman coding or error correction
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
    • H04L2209/00—Additional information or applications relating to cryptographic mechanisms or cryptographic arrangements for secret or secure communication H04L9/00
    • H04L2209/88—Medical equipments

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • General Health & Medical Sciences (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Physics & Mathematics (AREA)
  • Bioethics (AREA)
  • Databases & Information Systems (AREA)
  • Analytical Chemistry (AREA)
  • Chemical & Material Sciences (AREA)
  • General Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Data Mining & Analysis (AREA)
  • Software Systems (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Artificial Intelligence (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Signal Processing (AREA)
  • Computer Networks & Wireless Communication (AREA)
  • Computer Security & Cryptography (AREA)
  • Mathematical Analysis (AREA)
  • Mathematical Optimization (AREA)
  • Pure & Applied Mathematics (AREA)
  • Genetics & Genomics (AREA)
  • Mathematical Physics (AREA)
  • Computing Systems (AREA)
  • Human Computer Interaction (AREA)
  • Computational Mathematics (AREA)
  • Algebra (AREA)
  • Molecular Biology (AREA)
EP18753700.6A 2017-02-14 2018-02-14 METHOD AND DEVICE FOR COMPACT REPRESENTATION OF BIOINFORMATICS DATA USING SEVERAL GENOMIC DESCRIPTORS Pending EP3583500A4 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
PCT/US2017/017842 WO2018071055A1 (en) 2016-10-11 2017-02-14 Method and apparatus for the compact representation of bioinformatics data
PCT/US2017/041591 WO2018071080A2 (en) 2016-10-11 2017-07-11 Method and systems for the representation and processing of bioinformatics data using reference sequences
PCT/US2018/018092 WO2018152143A1 (en) 2017-02-14 2018-02-14 Method and apparatus for the compact representation of bioinformatics data using multiple genomic descriptors

Publications (2)

Publication Number Publication Date
EP3583500A1 EP3583500A1 (en) 2019-12-25
EP3583500A4 true EP3583500A4 (en) 2020-12-16

Family

ID=68609803

Family Applications (1)

Application Number Title Priority Date Filing Date
EP18753700.6A Pending EP3583500A4 (en) 2017-02-14 2018-02-14 METHOD AND DEVICE FOR COMPACT REPRESENTATION OF BIOINFORMATICS DATA USING SEVERAL GENOMIC DESCRIPTORS

Country Status (10)

Country Link
EP (1) EP3583500A4 (en)
KR (1) KR102733786B1 (en)
AU (1) AU2018221458B2 (en)
CA (1) CA3052824A1 (en)
EA (1) EA201991908A1 (en)
IL (1) IL268651A (en)
MX (1) MX2019009680A (en)
SG (1) SG11201907418YA (en)
WO (1) WO2018152143A1 (en)
ZA (1) ZA201905921B (en)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN110189830B (en) * 2019-05-24 2021-06-08 杭州火树科技有限公司 Electronic medical record word stock training method based on machine learning
EP3896698A1 (en) 2020-04-15 2021-10-20 Genomsys SA Method and system for the efficient data compression in mpeg-g
KR102497634B1 (en) * 2020-12-21 2023-02-08 부산대학교 산학협력단 Method and apparatus for compressing fastq data through character frequency-based sequence reordering
CN116206687A (en) * 2022-12-30 2023-06-02 深圳百人科技有限公司 Fuzzy matching k-mer coding mode

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150227686A1 (en) * 2014-02-12 2015-08-13 International Business Machines Corporation Lossless compression of dna sequences

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2002303234A1 (en) * 2001-04-02 2002-10-15 Cytoprint, Inc. Methods and apparatus for discovering, identifying and comparing biological activity mechanisms
US7698067B2 (en) * 2002-02-12 2010-04-13 International Business Machines Corporation Sequence pattern descriptors for transmembrane structural details
US7809765B2 (en) * 2007-08-24 2010-10-05 General Electric Company Sequence identification and analysis
KR101922129B1 (en) * 2011-12-05 2018-11-26 삼성전자주식회사 Method and apparatus for compressing and decompressing genetic information using next generation sequencing(NGS)
US9679104B2 (en) * 2013-01-17 2017-06-13 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
CN103336916B (en) * 2013-07-05 2016-04-06 中国科学院数学与系统科学研究院 A kind of sequencing sequence mapping method and system

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150227686A1 (en) * 2014-02-12 2015-08-13 International Business Machines Corporation Lossless compression of dna sequences

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
ANONYMOUS: "CRAM format specification (version 3.0)", 8 September 2016 (2016-09-08), XP002771305, Retrieved from the Internet <URL:https://samtools.github.io/hts-specs/CRAMv3.pdf> [retrieved on 20170622] *
See also references of WO2018152143A1 *

Also Published As

Publication number Publication date
KR102733786B1 (en) 2024-11-26
CA3052824A1 (en) 2018-08-23
AU2018221458A1 (en) 2019-10-03
EA201991908A1 (en) 2020-01-21
WO2018152143A1 (en) 2018-08-23
ZA201905921B (en) 2021-05-26
IL268651A (en) 2019-10-31
EP3583500A1 (en) 2019-12-25
MX2019009680A (en) 2019-10-09
AU2018221458B2 (en) 2022-12-08
NZ757185A (en) 2021-05-28
SG11201907418YA (en) 2019-09-27
KR20190113971A (en) 2019-10-08

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Owner name: KONINKLIJKE PHILIPS N.V.