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MX2019009682A - Metodo y sistemas para la reconstruccion de secuencias genomicas de referencia a partir de lecturas de secuencias genomicas comprimidas. - Google Patents

Metodo y sistemas para la reconstruccion de secuencias genomicas de referencia a partir de lecturas de secuencias genomicas comprimidas.

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Publication number
MX2019009682A
MX2019009682A MX2019009682A MX2019009682A MX2019009682A MX 2019009682 A MX2019009682 A MX 2019009682A MX 2019009682 A MX2019009682 A MX 2019009682A MX 2019009682 A MX2019009682 A MX 2019009682A MX 2019009682 A MX2019009682 A MX 2019009682A
Authority
MX
Mexico
Prior art keywords
syntax elements
compressed
reference genome
genomic sequences
aligned
Prior art date
Application number
MX2019009682A
Other languages
English (en)
Inventor
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/EP2016/074311 external-priority patent/WO2018068830A1/en
Priority claimed from PCT/EP2016/074307 external-priority patent/WO2018068829A1/en
Priority claimed from PCT/EP2016/074297 external-priority patent/WO2018068827A1/en
Priority claimed from PCT/EP2016/074301 external-priority patent/WO2018068828A1/en
Priority claimed from PCT/US2017/017842 external-priority patent/WO2018071055A1/en
Priority claimed from PCT/US2017/041579 external-priority patent/WO2018071078A1/en
Application filed by Genomsys Sa filed Critical Genomsys Sa
Publication of MX2019009682A publication Critical patent/MX2019009682A/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 OR CALCULATING; 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 OR CALCULATING; 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)
  • Theoretical Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Biotechnology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational 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)
  • Computer Security & Cryptography (AREA)
  • General Physics & Mathematics (AREA)
  • Computer Hardware Design (AREA)
  • Genetics & Genomics (AREA)
  • Data Mining & Analysis (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Technology Law (AREA)
  • Multimedia (AREA)
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  • Wood Science & Technology (AREA)
  • Biochemistry (AREA)
  • Evolutionary Computation (AREA)
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Abstract

El método y aparato descritos en esta divulgación incluyen representar un genoma de referencia en términos de elementos de sintaxis que describen las diferencias entre dicho genoma de referencia y secuencias genómicas previamente alineadas. Cada una de las secuencias genómicas alineadas se describe por medio de un subconjunto de elementos de sintaxis. Los elementos de sintaxis que describen todas las secuencias genómicas se dividen en bloques de acuerdo con sus propiedades estadísticas. Cada bloque de elementos de sintaxis se codifica por entropía. Los bloques codificados por entropía se concatenan luego para formar una corriente de bits comprimida. Las diferencias entre el genoma de referencia y las secuencias alineadas se expresan en términos de elementos de sintaxis, que se incrustan en la corriente de bits de bloques codificados de elementos de sintaxis que describen lecturas alineadas. El método descrito permite la reconstrucción del genoma de referencia utilizado para la alineación cuando se decodifican las secuencias genómicas comprimidas mientras se conservan diferentes opciones de acceso aleatorio en los datos comprimidos y se permite la compresión eficiente.
MX2019009682A 2016-10-11 2017-12-14 Metodo y sistemas para la reconstruccion de secuencias genomicas de referencia a partir de lecturas de secuencias genomicas comprimidas. MX2019009682A (es)

Applications Claiming Priority (9)

Application Number Priority Date Filing Date Title
PCT/EP2016/074311 WO2018068830A1 (en) 2016-10-11 2016-10-11 Method and system for the transmission of bioinformatics data
PCT/EP2016/074307 WO2018068829A1 (en) 2016-10-11 2016-10-11 Method and apparatus for compact representation of bioinformatics data
PCT/EP2016/074297 WO2018068827A1 (en) 2016-10-11 2016-10-11 Efficient data structures for bioinformatics information representation
PCT/EP2016/074301 WO2018068828A1 (en) 2016-10-11 2016-10-11 Method and system for storing and accessing bioinformatics data
EP2017017842 2017-02-14
PCT/US2017/017842 WO2018071055A1 (en) 2016-10-11 2017-02-14 Method and apparatus for the compact representation of bioinformatics data
EP2017017841 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/US2017/066458 WO2018151786A1 (en) 2016-10-11 2017-12-14 Method and systems for the reconstruction of genomic reference sequences from compressed genomic sequence reads

Publications (1)

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MX2019009682A true MX2019009682A (es) 2019-10-09

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Family Applications (3)

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MX2019004131A MX2019004131A (es) 2016-10-11 2017-07-11 Metodo y aparato para el acceso a datos bioinformaticos estructurados en unidades de acceso.
MX2019004129A MX2019004129A (es) 2016-10-11 2017-07-11 Metodo y sistemas para la indexacion de datos bioinformaticos.
MX2019009682A MX2019009682A (es) 2016-10-11 2017-12-14 Metodo y sistemas para la reconstruccion de secuencias genomicas de referencia a partir de lecturas de secuencias genomicas comprimidas.

Family Applications Before (2)

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MX2019004131A MX2019004131A (es) 2016-10-11 2017-07-11 Metodo y aparato para el acceso a datos bioinformaticos estructurados en unidades de acceso.
MX2019004129A MX2019004129A (es) 2016-10-11 2017-07-11 Metodo y sistemas para la indexacion de datos bioinformaticos.

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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) IL268649B2 (es)
MX (3) MX2019004131A (es)
PH (1) PH12019501880A1 (es)
SG (2) SG11201903269QA (es)
WO (1) WO2018151786A1 (es)

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KR102497634B1 (ko) * 2020-12-21 2023-02-08 부산대학교 산학협력단 문자 빈도 기반 서열 재정렬을 통한 fastq 데이터 압축 방법 및 장치
CN115458050B (zh) * 2022-08-05 2026-01-06 武汉大学 多基因发现网络构造方法、装置、设备及存储介质

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MX2019004129A (es) 2019-08-29
CA3040057A1 (en) 2018-04-19
IL268649B1 (en) 2024-03-01
IL268650B1 (en) 2024-03-01
CA3052773A1 (en) 2018-08-23
AU2017342754A1 (en) 2019-05-02
IL268650B2 (en) 2024-07-01
CL2019000971A1 (es) 2019-08-23
SG11201907415SA (en) 2019-09-27
MX2019004131A (es) 2020-01-30
EP3583249A1 (en) 2019-12-25
KR102421458B1 (ko) 2022-07-14
KR20190062551A (ko) 2019-06-05
IL268650A (en) 2019-10-31
PH12019501880A1 (en) 2020-06-29
US11763918B2 (en) 2023-09-19
IL265956A (en) 2019-05-30
EP3583249A4 (en) 2020-12-02
IL268649B2 (en) 2024-07-01
IL268649A (en) 2019-10-31
EP3583249B1 (en) 2023-07-19
SG11201903269QA (en) 2019-05-30
WO2018151786A1 (en) 2018-08-23
KR102729412B1 (ko) 2024-11-13
AU2017398951A1 (en) 2019-10-10
KR20190113969A (ko) 2019-10-08
US20200043570A1 (en) 2020-02-06
CO2019009919A2 (es) 2019-12-10

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