CL2019002275A1 - Método y sistemas para la reconstrucción de secuencias genómicas de referencia a partir de lecturas de secuencias genómicas comprimidas. - Google Patents

Método y sistemas para la reconstrucción de secuencias genómicas de referencia a partir de lecturas de secuencias genómicas comprimidas.

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Publication number
CL2019002275A1
CL2019002275A1 CL2019002275A CL2019002275A CL2019002275A1 CL 2019002275 A1 CL2019002275 A1 CL 2019002275A1 CL 2019002275 A CL2019002275 A CL 2019002275A CL 2019002275 A CL2019002275 A CL 2019002275A CL 2019002275 A1 CL2019002275 A1 CL 2019002275A1
Authority
CL
Chile
Prior art keywords
genomic sequences
syntax elements
reference genome
compressed
aligned
Prior art date
Application number
CL2019002275A
Other languages
English (en)
Inventor
Claudio Alberti
Mohamed Khoso Baluch
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/EP2016/074297 external-priority patent/WO2018068827A1/en
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/EP2016/074301 external-priority patent/WO2018068828A1/en
Priority claimed from PCT/US2017/041579 external-priority patent/WO2018071078A1/en
Application filed by Genomsys Sa filed Critical Genomsys Sa
Publication of CL2019002275A1 publication Critical patent/CL2019002275A1/es

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    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/22—Indexing; Data structures therefor; Storage structures
    • G06F16/2282—Tablespace storage structures; Management thereof
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/23—Updating
    • G06F16/2365—Ensuring data consistency and integrity
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/28—Databases characterised by their database models, e.g. relational or object models
    • G06F16/284—Relational databases
    • G06F16/285—Clustering or classification
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
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    • G06F21/00—Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
    • G06F21/60—Protecting data
    • G06F21/602—Providing cryptographic facilities or services
    • 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
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
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    • 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
    • G06—COMPUTING OR CALCULATING; COUNTING
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    • 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
    • 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
    • G16B20/10—Ploidy or copy number detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
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    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
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    • 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
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    • G16B30/20—Sequence assembly
    • G—PHYSICS
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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
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    • 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
    • G16B50/10—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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/40—Encryption 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
    • 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
    • G16B99/00—Subject matter not provided for in other groups of this subclass
    • 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
    • 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)
  • Bioinformatics & Cheminformatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Biophysics (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Physics & Mathematics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Chemical & Material Sciences (AREA)
  • Data Mining & Analysis (AREA)
  • Software Systems (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Computer Security & Cryptography (AREA)
  • Computer Hardware Design (AREA)
  • Artificial Intelligence (AREA)
  • Public Health (AREA)
  • Evolutionary Computation (AREA)
  • Epidemiology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Human Computer Interaction (AREA)
  • Signal Processing (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Compression, Expansion, Code Conversion, And Decoders (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Detection And Prevention Of Errors In Transmission (AREA)
  • Television Signal Processing For Recording (AREA)

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.
CL2019002275A 2016-10-11 2019-08-12 Método y sistemas para la reconstrucción de secuencias genómicas de referencia a partir de lecturas de secuencias genómicas comprimidas. CL2019002275A1 (es)

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
PCT/EP2016/074297 WO2018068827A1 (en) 2016-10-11 2016-10-11 Efficient data structures for bioinformatics information representation
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/EP2016/074301 WO2018068828A1 (en) 2016-10-11 2016-10-11 Method and system for storing and accessing bioinformatics data
PCT/US2017/017842 WO2018071055A1 (en) 2016-10-11 2017-02-14 Method and apparatus for the compact representation of bioinformatics data
PCT/US2017/041579 WO2018071078A1 (en) 2016-10-11 2017-07-11 Method and apparatus for the access to bioinformatics data structured in access units

Publications (1)

Publication Number Publication Date
CL2019002275A1 true CL2019002275A1 (es) 2019-11-22

Family

ID=61905752

Family Applications (6)

Application Number Title Priority Date Filing Date
CL2019000972A CL2019000972A1 (es) 2016-10-11 2019-04-10 Método y sistemas para la representación y procesamiento de datos de bioinformática mediante el uso de secuencias de referencia.
CL2019000973A CL2019000973A1 (es) 2016-10-11 2019-04-10 Método y sistemas para la indexación de datos bioinformáticos.
CL2019000968A CL2019000968A1 (es) 2016-10-11 2019-04-10 Método y sistema para el acceso selectivo de datos bioinformáticos almacenados o transmitidos.
CL2019002275A CL2019002275A1 (es) 2016-10-11 2019-08-12 Método y sistemas para la reconstrucción de secuencias genómicas de referencia a partir de lecturas de secuencias genómicas comprimidas.
CL2019002276A CL2019002276A1 (es) 2016-10-11 2019-08-12 Método y sistemas para la compresión eficiente de lecturas de secuencias genómicas.
CL2019002277A CL2019002277A1 (es) 2016-10-11 2019-08-12 Método y aparato para la representación compacta de datos de bioinformática mediante el uso de múltiples descriptores genómicos.

Family Applications Before (3)

Application Number Title Priority Date Filing Date
CL2019000972A CL2019000972A1 (es) 2016-10-11 2019-04-10 Método y sistemas para la representación y procesamiento de datos de bioinformática mediante el uso de secuencias de referencia.
CL2019000973A CL2019000973A1 (es) 2016-10-11 2019-04-10 Método y sistemas para la indexación de datos bioinformáticos.
CL2019000968A CL2019000968A1 (es) 2016-10-11 2019-04-10 Método y sistema para el acceso selectivo de datos bioinformáticos almacenados o transmitidos.

Family Applications After (2)

Application Number Title Priority Date Filing Date
CL2019002276A CL2019002276A1 (es) 2016-10-11 2019-08-12 Método y sistemas para la compresión eficiente de lecturas de secuencias genómicas.
CL2019002277A CL2019002277A1 (es) 2016-10-11 2019-08-12 Método y aparato para la representación compacta de datos de bioinformática mediante el uso de múltiples descriptores genómicos.

Country Status (17)

Country Link
US (6) US20200042735A1 (es)
EP (3) EP3526694A4 (es)
JP (4) JP2020505702A (es)
KR (4) KR20190073426A (es)
CN (6) CN110168651A (es)
AU (3) AU2017342688A1 (es)
BR (7) BR112019007359A2 (es)
CA (3) CA3040138A1 (es)
CL (6) CL2019000972A1 (es)
CO (6) CO2019003595A2 (es)
EA (2) EA201990917A1 (es)
IL (3) IL265879B2 (es)
MX (2) MX2019004130A (es)
PE (7) PE20191058A1 (es)
PH (6) PH12019550058A1 (es)
SG (3) SG11201903270RA (es)
WO (4) WO2018071054A1 (es)

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