CL2019000954A1 - Estructuras eficientes de datos para la representación de información bioinformática. - Google Patents

Estructuras eficientes de datos para la representación de información bioinformática.

Info

Publication number
CL2019000954A1
CL2019000954A1 CL2019000954A CL2019000954A CL2019000954A1 CL 2019000954 A1 CL2019000954 A1 CL 2019000954A1 CL 2019000954 A CL2019000954 A CL 2019000954A CL 2019000954 A CL2019000954 A CL 2019000954A CL 2019000954 A1 CL2019000954 A1 CL 2019000954A1
Authority
CL
Chile
Prior art keywords
representation
data structures
efficient data
bioinformatics information
aligned
Prior art date
Application number
CL2019000954A
Other languages
English (en)
Inventor
Daniele Renzi
Giorgio Zoia
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
Application filed by Genomsys Sa filed Critical Genomsys Sa
Publication of CL2019000954A1 publication Critical patent/CL2019000954A1/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
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • 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
    • 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
    • G16B50/30—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

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Theoretical Computer Science (AREA)
  • Biotechnology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Genetics & Genomics (AREA)
  • Bioethics (AREA)
  • Databases & Information Systems (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Chemical & Material Sciences (AREA)
  • Molecular Biology (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Compression, Expansion, Code Conversion, And Decoders (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

MÉTODO Y APARATO PARA LA REPRESENTACIÓN DE DATOS DE SECUENCIA DEL GENOMA ORGANIZADOS EN UN FORMATO DE ARCHIVO ESTRUCTURADO. LA ESTRUCTURA DE DATOS CONTIENE LA REPRESENTACIÓN DE SECUENCIAS DE NUCLEÓTIDOS: EN FORMA COMPRIMIDA, ALINEADAS Y REFERENCIADAS A UNA O MÁS SECUENCIAS DE REFERENCIA Y CLASIFICADAS SEGÚN DIFERENTES GRADOS DE PRECISIÓN DE COINCIDENCIA. LAS LECTURAS CLASIFICADAS Y ALINEADAS SE CODIFICAN EN FORMA DE CAPAS DE ELEMENTOS DE SINTAXIS, QUE INCLUYEN INFORMACIÓN DE ENCABEZADO Y SE DIVIDEN EN UNIDADES DE ACCESO INDEPENDIENTES O DEPENDIENTES.
CL2019000954A 2016-10-11 2019-04-09 Estructuras eficientes de datos para la representación de información bioinformática. CL2019000954A1 (es)

Applications Claiming Priority (1)

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

Publications (1)

Publication Number Publication Date
CL2019000954A1 true CL2019000954A1 (es) 2019-08-23

Family

ID=57233388

Family Applications (1)

Application Number Title Priority Date Filing Date
CL2019000954A CL2019000954A1 (es) 2016-10-11 2019-04-09 Estructuras eficientes de datos para la representación de información bioinformática.

Country Status (20)

Country Link
US (1) US20210304841A1 (es)
EP (2) EP4075438B1 (es)
JP (1) JP6902104B2 (es)
KR (1) KR102807240B1 (es)
CN (1) CN110088839B (es)
AU (1) AU2016426569B2 (es)
BR (1) BR112019007296A2 (es)
CA (1) CA3039688C (es)
CL (1) CL2019000954A1 (es)
CO (1) CO2019003583A2 (es)
EA (1) EA201990933A1 (es)
ES (2) ES2973590T3 (es)
FI (1) FI4075438T3 (es)
IL (1) IL265908B2 (es)
MX (1) MX2019004125A (es)
PH (1) PH12019500791A1 (es)
PL (2) PL4075438T3 (es)
SG (1) SG11201903175VA (es)
WO (1) WO2018068827A1 (es)
ZA (1) ZA201902785B (es)

Families Citing this family (9)

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Publication number Priority date Publication date Assignee Title
US20200104463A1 (en) * 2018-09-28 2020-04-02 Chris Glode Genomic network service user interface
CN110060742B (zh) * 2019-03-15 2023-07-25 南京派森诺基因科技有限公司 一种gtf文件解析方法及工具
CN114503206A (zh) * 2019-10-01 2022-05-13 皇家飞利浦有限公司 用于在基因组图中有效识别和提取序列路径的系统和方法
JP7848681B2 (ja) * 2019-10-18 2026-04-21 コーニンクレッカ フィリップス エヌ ヴェ カスタマイズ可能な区切りテキスト圧縮フレームワーク
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
US12014802B2 (en) * 2020-03-17 2024-06-18 Western Digital Technologies, Inc. Devices and methods for locating a sample read in a reference genome
EP3896698A1 (en) 2020-04-15 2021-10-20 Genomsys SA Method and system for the efficient data compression in mpeg-g
US12406413B2 (en) * 2021-05-10 2025-09-02 Optum Services (Ireland) Limited Predictive data analysis using image representations of genomic data
CN113643761B (zh) * 2021-10-13 2022-01-18 苏州赛美科基因科技有限公司 一种用于解读二代测序结果所需数据的提取方法

Family Cites Families (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1547009A1 (en) * 2002-09-20 2005-06-29 Board Of Regents The University Of Texas System Computer program products, systems and methods for information discovery and relational analyses
KR101969848B1 (ko) * 2011-06-10 2019-04-17 삼성전자주식회사 유전자 데이터를 압축하는 방법 및 장치
KR101188886B1 (ko) * 2010-10-22 2012-10-09 삼성에스디에스 주식회사 유전 정보 관리 시스템 및 방법
KR101253700B1 (ko) * 2010-11-26 2013-04-12 가천대학교 산학협력단 Ｎｇｓ 데이터의 고속 압축장치 및 그 방법
US20130246460A1 (en) * 2011-03-09 2013-09-19 Annai Systems, Inc. System and method for facilitating network-based transactions involving sequence data
EP2718862B1 (en) * 2011-06-06 2018-10-31 Koninklijke Philips N.V. Method for assembly of nucleic acid sequence data
KR101922129B1 (ko) * 2011-12-05 2018-11-26 삼성전자주식회사 차세대 시퀀싱을 이용하여 획득된 유전 정보를 압축 및 압축해제하는 방법 및 장치
US9092402B2 (en) * 2013-10-21 2015-07-28 Seven Bridges Genomics Inc. Systems and methods for using paired-end data in directed acyclic structure
US10902937B2 (en) * 2014-02-12 2021-01-26 International Business Machines Corporation Lossless compression of DNA sequences
WO2016141294A1 (en) * 2015-03-05 2016-09-09 Seven Bridges Genomics Inc. Systems and methods for genomic pattern analysis
EP4235680A3 (en) * 2016-10-11 2023-10-11 Genomsys SA Method and apparatus for compact representation of bioinformatics data

Also Published As

Publication number Publication date
CN110088839A (zh) 2019-08-02
IL265908A (en) 2019-06-30
IL265908B2 (en) 2024-09-01
CO2019003583A2 (es) 2019-08-30
BR112019007296A2 (pt) 2019-09-17
KR20190062544A (ko) 2019-06-05
CN110088839B (zh) 2023-12-15
CA3039688A1 (en) 2018-04-19
EA201990933A1 (ru) 2019-11-29
KR102807240B1 (ko) 2025-05-14
ZA201902785B (en) 2020-11-25
SG11201903175VA (en) 2019-05-30
PL4075438T3 (pl) 2024-08-05
WO2018068827A1 (en) 2018-04-19
EP3526709B1 (en) 2022-04-20
EP4075438A1 (en) 2022-10-19
ES2973590T3 (es) 2024-06-20
FI4075438T3 (fi) 2024-03-14
AU2016426569A1 (en) 2019-06-06
NZ753247A (en) 2021-09-24
US20210304841A1 (en) 2021-09-30
JP6902104B2 (ja) 2021-07-14
JP2019537810A (ja) 2019-12-26
MX2019004125A (es) 2019-06-10
PL3526709T3 (pl) 2022-09-26
EP3526709A1 (en) 2019-08-21
AU2016426569B2 (en) 2023-08-17
EP4075438B1 (en) 2023-12-13
IL265908B1 (en) 2024-05-01
PH12019500791A1 (en) 2019-12-11
CA3039688C (en) 2024-03-19
ES2922420T3 (es) 2022-09-14

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