EA201991908A1 - METHOD AND DEVICE FOR COMPACT REPRESENTATION OF BIOINFORMATION DATA BY USING MULTIPLE GENOMIC DESCRIPTORS - Google Patents

METHOD AND DEVICE FOR COMPACT REPRESENTATION OF BIOINFORMATION DATA BY USING MULTIPLE GENOMIC DESCRIPTORS

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Publication number
EA201991908A1
EA201991908A1 EA201991908A EA201991908A EA201991908A1 EA 201991908 A1 EA201991908 A1 EA 201991908A1 EA 201991908 A EA201991908 A EA 201991908A EA 201991908 A EA201991908 A EA 201991908A EA 201991908 A1 EA201991908 A1 EA 201991908A1
Authority
EA
Eurasian Patent Office
Prior art keywords
data
compact representation
multiple genomic
descriptors
reads
Prior art date
Application number
EA201991908A
Other languages
Russian (ru)
Inventor
Клаудио Алберти
Гиоргио Зоиа
Даниэле Рензи
Мохамед Хосо Балуч
Original Assignee
Геномсыс Са
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 Геномсыс Са filed Critical Геномсыс Са
Publication of EA201991908A1 publication Critical patent/EA201991908A1/en

Links

Classifications

    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR 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
    • 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; CALCULATING OR 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; CALCULATING OR 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
    • 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
    • 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
    • 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
    • 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)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • General Physics & Mathematics (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • General Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Data Mining & Analysis (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
  • Software Systems (AREA)
  • Evolutionary Computation (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Artificial Intelligence (AREA)
  • Computer Security & Cryptography (AREA)
  • Mathematical Analysis (AREA)
  • Computer Networks & Wireless Communication (AREA)
  • Mathematical Optimization (AREA)
  • Pure & Applied Mathematics (AREA)
  • Signal Processing (AREA)
  • Genetics & Genomics (AREA)
  • Computational Mathematics (AREA)
  • Algebra (AREA)
  • Human Computer Interaction (AREA)
  • Mathematical Physics (AREA)
  • Computing Systems (AREA)
  • Molecular Biology (AREA)

Abstract

Способ и устройство для сжатия данных геномной последовательности, созданных секвенаторами генома. Прочтения последовательности кодируют путем выравнивания их относительно ранее существующих или построенных референсных последовательностей, причем процесс кодирования состоит из классифицирования прочтений в классы данных с последующим кодированием каждого класса посредством множества блоков дескрипторов. Для каждого класса данных, на которые разбивают данные, и каждого соответствующего блока дескрипторов используют специальные модели источников и энтропийные кодеры.Method and apparatus for compressing genomic sequence data generated by genome sequencers. The reads of the sequence are encoded by aligning them with respect to previously existing or constructed reference sequences, and the coding process consists of classifying the reads into data classes, followed by encoding each class by means of a plurality of descriptor blocks. For each class of data into which the data is split and each corresponding block of descriptors, special source models and entropy encoders are used.

EA201991908A 2017-02-14 2018-02-14 METHOD AND DEVICE FOR COMPACT REPRESENTATION OF BIOINFORMATION DATA BY USING MULTIPLE GENOMIC DESCRIPTORS EA201991908A1 (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 (1)

Publication Number Publication Date
EA201991908A1 true EA201991908A1 (en) 2020-01-21

Family

ID=68609803

Family Applications (1)

Application Number Title Priority Date Filing Date
EA201991908A EA201991908A1 (en) 2017-02-14 2018-02-14 METHOD AND DEVICE FOR COMPACT REPRESENTATION OF BIOINFORMATION DATA BY USING MULTIPLE GENOMIC DESCRIPTORS

Country Status (10)

Country Link
EP (1) EP3583500A4 (en)
KR (1) KR20190113971A (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 (3)

* 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

Family Cites Families (7)

* 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
US10902937B2 (en) * 2014-02-12 2021-01-26 International Business Machines Corporation Lossless compression of DNA sequences

Also Published As

Publication number Publication date
SG11201907418YA (en) 2019-09-27
IL268651A (en) 2019-10-31
NZ757185A (en) 2021-05-28
CA3052824A1 (en) 2018-08-23
KR20190113971A (en) 2019-10-08
ZA201905921B (en) 2021-05-26
AU2018221458B2 (en) 2022-12-08
WO2018152143A1 (en) 2018-08-23
EP3583500A1 (en) 2019-12-25
MX2019009680A (en) 2019-10-09
AU2018221458A1 (en) 2019-10-03
EP3583500A4 (en) 2020-12-16

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