CO2019003595A2 - Método y sistemas para la representación y procesamiento de datos de bioinformática mediante el uso de secuencias de referencia - Google Patents

Método y sistemas para la representación y procesamiento de datos de bioinformática mediante el uso de secuencias de referencia

Info

Publication number
CO2019003595A2
CO2019003595A2 CONC2019/0003595A CO2019003595A CO2019003595A2 CO 2019003595 A2 CO2019003595 A2 CO 2019003595A2 CO 2019003595 A CO2019003595 A CO 2019003595A CO 2019003595 A2 CO2019003595 A2 CO 2019003595A2
Authority
CO
Colombia
Prior art keywords
data
reference sequences
representation
processing
coding
Prior art date
Application number
CONC2019/0003595A
Other languages
English (en)
Inventor
Giorgio Zoia
Daniele Renzi
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/EP2016/074311 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/EP2016/074297 external-priority patent/WO2018068827A1/en
Application filed by Genomsys Sa filed Critical Genomsys Sa
Publication of CO2019003595A2 publication Critical patent/CO2019003595A2/es

Links

Classifications

    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR 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; CALCULATING OR 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; CALCULATING OR 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; 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
    • G06F21/602—Providing cryptographic facilities or services
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • G16B50/10—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

Abstract

Método y aparato para la representación y procesamiento de datos de secuencia del genoma, producidos por máquinas de secuenciación del genoma, cuando se alinean en una o más secuencias de referencia. Las lecturas de secuencia se codifican al alinearlas con respecto a las secuencias de referencia preexistentes o construidas. Después de la alineación, el proceso de codificación se compone de una clasificación de las lecturas en clases de datos, seguida de la codificación de cada clase de datos en términos de una multiplicidad de capas de descriptores. Se utilizan modelos de fuente específicos y codificadores de entropía para la codificación de los subconjuntos de descriptores utilizados para representar cada clase de datos.
CONC2019/0003595A 2016-10-11 2019-04-11 Método y sistemas para la representación y procesamiento de datos de bioinformática mediante el uso de secuencias de referencia CO2019003595A2 (es)

Applications Claiming Priority (5)

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/EP2016/074301 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
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

Publications (1)

Publication Number Publication Date
CO2019003595A2 true CO2019003595A2 (es) 2019-08-30

Family

ID=61905752

Family Applications (6)

Application Number Title Priority Date Filing Date
CONC2019/0003638A CO2019003638A2 (es) 2016-10-11 2019-04-11 Método y aparato para el acceso a datos bioinformáticos estructurados en unidades de acceso
CONC2019/0003639A CO2019003639A2 (es) 2016-10-11 2019-04-11 Método y sistemas para la indexación de datos bioinformáticos
CONC2019/0003595A CO2019003595A2 (es) 2016-10-11 2019-04-11 Método y sistemas para la representación y procesamiento de datos de bioinformática mediante el uso de secuencias de referencia
CONC2019/0003842A CO2019003842A2 (es) 2016-10-11 2019-04-15 Método y sistema para el acceso selectivo de datos bioinformáticos almacenados o transmitidos
CONC2019/0009920A CO2019009920A2 (es) 2016-10-11 2019-09-12 Método y aparato para la representación compacta de datos de bioinformática mediante el uso de múltiples descriptores genómicos
CONC2019/0009922A CO2019009922A2 (es) 2016-10-11 2019-09-12 Método y sistemas para la reconstrucción de secuencias genómicas de referencia a partir de lecturas de secuencias genómicas comprimidas

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Application Number Title Priority Date Filing Date
CONC2019/0003638A CO2019003638A2 (es) 2016-10-11 2019-04-11 Método y aparato para el acceso a datos bioinformáticos estructurados en unidades de acceso
CONC2019/0003639A CO2019003639A2 (es) 2016-10-11 2019-04-11 Método y sistemas para la indexación de datos bioinformáticos

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CONC2019/0003842A CO2019003842A2 (es) 2016-10-11 2019-04-15 Método y sistema para el acceso selectivo de datos bioinformáticos almacenados o transmitidos
CONC2019/0009920A CO2019009920A2 (es) 2016-10-11 2019-09-12 Método y aparato para la representación compacta de datos de bioinformática mediante el uso de múltiples descriptores genómicos
CONC2019/0009922A CO2019009922A2 (es) 2016-10-11 2019-09-12 Método y sistemas para la reconstrucción de secuencias genómicas de referencia a partir de lecturas de secuencias genómicas comprimidas

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) CO2019003638A2 (es)
EA (2) EA201990917A1 (es)
IL (3) IL265879B2 (es)
MX (2) MX2019004130A (es)
PE (7) PE20191058A1 (es)
PH (6) PH12019550057A1 (es)
SG (3) SG11201903270RA (es)
WO (4) WO2018071055A1 (es)

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