CO2019009919A2 - Método y sistemas para la compresión eficiente de lecturas de secuencias genómicas - Google Patents

Método y sistemas para la compresión eficiente de lecturas de secuencias genómicas

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Publication number
CO2019009919A2
CO2019009919A2 CO2019009919A CO2019009919A CO2019009919A2 CO 2019009919 A2 CO2019009919 A2 CO 2019009919A2 CO 2019009919 A CO2019009919 A CO 2019009919A CO 2019009919 A CO2019009919 A CO 2019009919A CO 2019009919 A2 CO2019009919 A2 CO 2019009919A2
Authority
CO
Colombia
Prior art keywords
sequence reads
systems
encoding
genomic sequence
efficient compression
Prior art date
Application number
CO2019009919A
Other languages
English (en)
Inventor
Mohamed Khoso Baluch
Claudio Alberti
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
Priority claimed from PCT/US2017/017842 external-priority patent/WO2018071055A1/en
Priority claimed from PCT/US2017/041579 external-priority patent/WO2018071078A1/en
Priority claimed from PCT/US2017/066863 external-priority patent/WO2018151788A1/en
Application filed by Genomsys Sa filed Critical Genomsys Sa
Publication of CO2019009919A2 publication Critical patent/CO2019009919A2/es

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    • 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

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  • 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

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 descriptores genómicos. Los descriptores genómicos del mismo tipo se organizan en bloques que se comprimen mediante la aplicación de sucesivas etapas de transformación, binarización y codificación de entropía. Se utilizan modelos de fuente y codificadores de entropía específicos para cada clase de datos y para cada descriptor asociado.
CO2019009919A 2016-10-11 2019-09-12 Método y sistemas para la compresión eficiente de lecturas de secuencias genómicas CO2019009919A2 (es)

Applications Claiming Priority (9)

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
PCT/US2017/017842 WO2018071055A1 (en) 2016-10-11 2017-02-14 Method and apparatus for the compact representation of bioinformatics data
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
PCT/US2017/066863 WO2018151788A1 (en) 2017-02-14 2017-12-15 Method and systems for the efficient compression of genomic sequence reads

Publications (1)

Publication Number Publication Date
CO2019009919A2 true CO2019009919A2 (es) 2019-12-10

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CO2019009919A CO2019009919A2 (es) 2016-10-11 2019-09-12 Método y sistemas para la compresión eficiente de lecturas de secuencias genómicas

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US (1) US11763918B2 (es)
EP (1) EP3583249B1 (es)
KR (2) KR102421458B1 (es)
AU (2) AU2017342754A1 (es)
CA (2) CA3040057A1 (es)
CL (1) CL2019000971A1 (es)
CO (1) CO2019009919A2 (es)
IL (3) IL268649B1 (es)
MX (3) MX2019004129A (es)
PH (1) PH12019501880A1 (es)
SG (2) SG11201903269QA (es)
WO (1) WO2018151786A1 (es)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
US20200104463A1 (en) * 2018-09-28 2020-04-02 Chris Glode Genomic network service user interface
CN111326216B (zh) * 2020-02-27 2023-07-21 中国科学院计算技术研究所 一种针对大数据基因测序文件的快速划分方法
KR102497634B1 (ko) * 2020-12-21 2023-02-08 부산대학교 산학협력단 문자 빈도 기반 서열 재정렬을 통한 fastq 데이터 압축 방법 및 장치

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EP3583249A4 (en) 2020-12-02
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 (es) 2020-01-30
MX2019004129A (es) 2019-08-29
CA3040057A1 (en) 2018-04-19
IL268649B1 (en) 2024-03-01
SG11201903269QA (en) 2019-05-30
KR20190062551A (ko) 2019-06-05
KR20190113969A (ko) 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 (ko) 2022-07-14
EP3583249B1 (en) 2023-07-19
CL2019000971A1 (es) 2019-08-23
IL268650A (en) 2019-10-31
MX2019009682A (es) 2019-10-09
IL268649A (en) 2019-10-31
IL265956A (en) 2019-05-30

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