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MX2019009680A - Metodo y aparato para la representacion compacta de datos de bioinformatica mediante el uso de multiples descriptores genomicos. - Google Patents

Metodo y aparato para la representacion compacta de datos de bioinformatica mediante el uso de multiples descriptores genomicos.

Info

Publication number
MX2019009680A
MX2019009680A MX2019009680A MX2019009680A MX2019009680A MX 2019009680 A MX2019009680 A MX 2019009680A MX 2019009680 A MX2019009680 A MX 2019009680A MX 2019009680 A MX2019009680 A MX 2019009680A MX 2019009680 A MX2019009680 A MX 2019009680A
Authority
MX
Mexico
Prior art keywords
data
compact representation
multiple genomic
bioinformatics data
class
Prior art date
Application number
MX2019009680A
Other languages
English (en)
Inventor
Zoia Giorgio
Renzi Daniele
Khoso Baluch Mohamed
Alberti Claudio
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 MX2019009680A publication Critical patent/MX2019009680A/es

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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/50—Compression of genetic data
    • 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
    • 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
    • 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
    • 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)
  • Biotechnology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Evolutionary Biology (AREA)
  • Biophysics (AREA)
  • General Physics & Mathematics (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • General Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Chemical & Material Sciences (AREA)
  • Data Mining & Analysis (AREA)
  • Software Systems (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Computer Networks & Wireless Communication (AREA)
  • Computer Security & Cryptography (AREA)
  • Mathematical Optimization (AREA)
  • Signal Processing (AREA)
  • Mathematical Analysis (AREA)
  • Pure & Applied Mathematics (AREA)
  • Genetics & Genomics (AREA)
  • Mathematical Physics (AREA)
  • Computing Systems (AREA)
  • Algebra (AREA)
  • Molecular Biology (AREA)
  • Computational Mathematics (AREA)
  • Human Computer Interaction (AREA)

Abstract

Método y aparato para la compresión de datos de secuencias de genomas producidos por máquinas de secuenciación del genoma. Las lecturas de secuencias se codifican mediante su alineación con respecto a secuencias de referencia preexistentes o construidas, en donde el proceso de codificación está compuesto por una clasificación de las lecturas en clases de datos, a lo cual sigue la codificación de cada clase en términos de una multiplicidad de bloques de descriptores. Se utilizan modelos fuente y codificadores de entropía específicos para cada clase de datos en los que se dividen los datos y para cada bloque de descriptor asociado.
MX2019009680A 2017-02-14 2018-02-14 Metodo y aparato para la representacion compacta de datos de bioinformatica mediante el uso de multiples descriptores genomicos. MX2019009680A (es)

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
MX2019009680A true MX2019009680A (es) 2019-10-09

Family

ID=68609803

Family Applications (1)

Application Number Title Priority Date Filing Date
MX2019009680A MX2019009680A (es) 2017-02-14 2018-02-14 Metodo y aparato para la representacion compacta de datos de bioinformatica mediante el uso de multiples descriptores genomicos.

Country Status (10)

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

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN110189830B (zh) * 2019-05-24 2021-06-08 杭州火树科技有限公司 基于机器学习的电子病历词库训练方法
EP3896698A1 (en) 2020-04-15 2021-10-20 Genomsys SA Method and system for the efficient data compression in mpeg-g
KR102497634B1 (ko) * 2020-12-21 2023-02-08 부산대학교 산학협력단 문자 빈도 기반 서열 재정렬을 통한 fastq 데이터 압축 방법 및 장치
CN116206687A (zh) * 2022-12-30 2023-06-02 深圳百人科技有限公司 一种模糊匹配的k-mer编码方式

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20020159625A1 (en) * 2001-04-02 2002-10-31 Cytoprint, Inc. Method 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 (ko) * 2011-12-05 2018-11-26 삼성전자주식회사 차세대 시퀀싱을 이용하여 획득된 유전 정보를 압축 및 압축해제하는 방법 및 장치
US9679104B2 (en) * 2013-01-17 2017-06-13 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
CN103336916B (zh) * 2013-07-05 2016-04-06 中国科学院数学与系统科学研究院 一种测序序列映射方法及系统
US10902937B2 (en) * 2014-02-12 2021-01-26 International Business Machines Corporation Lossless compression of DNA sequences

Also Published As

Publication number Publication date
NZ757185A (en) 2021-05-28
EP3583500A1 (en) 2019-12-25
AU2018221458B2 (en) 2022-12-08
WO2018152143A1 (en) 2018-08-23
KR102733786B1 (ko) 2024-11-26
EP3583500A4 (en) 2020-12-16
CA3052824A1 (en) 2018-08-23
SG11201907418YA (en) 2019-09-27
IL268651A (en) 2019-10-31
KR20190113971A (ko) 2019-10-08
ZA201905921B (en) 2021-05-26
EA201991908A1 (ru) 2020-01-21
AU2018221458A1 (en) 2019-10-03

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