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CO2019009922A2 - 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

Info

Publication number
CO2019009922A2
CO2019009922A2 CONC2019/0009922A CO2019009922A CO2019009922A2 CO 2019009922 A2 CO2019009922 A2 CO 2019009922A2 CO 2019009922 A CO2019009922 A CO 2019009922A CO 2019009922 A2 CO2019009922 A2 CO 2019009922A2
Authority
CO
Colombia
Prior art keywords
genomic sequences
syntax elements
reference genome
compressed
aligned
Prior art date
Application number
CONC2019/0009922A
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/EP2016/074311 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/US2017/041579 external-priority patent/WO2018071078A1/en
Priority claimed from PCT/US2017/066458 external-priority patent/WO2018151786A1/en
Application filed by Genomsys Sa filed Critical Genomsys Sa
Publication of CO2019009922A2 publication Critical patent/CO2019009922A2/es

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    • 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
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    • 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)
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  • General Health & Medical Sciences (AREA)
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  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
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  • Television Signal Processing For Recording (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.
CONC2019/0009922A 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 CO2019009922A2 (es)

Applications Claiming Priority (7)

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
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
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)

Publication Number Publication Date
CO2019009922A2 true CO2019009922A2 (es) 2020-01-17

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Family Applications (6)

Application Number Title Priority Date Filing Date
CONC2019/0003639A CO2019003639A2 (es) 2016-10-11 2019-04-11 Método y sistemas para la indexación de datos bioinformáticos
CONC2019/0003638A CO2019003638A2 (es) 2016-10-11 2019-04-11 Método y aparato para el acceso a datos bioinformáticos estructurados en unidades de acceso
CONC2019/0003595A 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
CONC2019/0003639A CO2019003639A2 (es) 2016-10-11 2019-04-11 Método y sistemas para la indexación de datos bioinformáticos
CONC2019/0003638A CO2019003638A2 (es) 2016-10-11 2019-04-11 Método y aparato para el acceso a datos bioinformáticos estructurados en unidades de acceso
CONC2019/0003595A 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

Country Status (17)

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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) CO2019003639A2 (es)
EA (2) EA201990916A1 (es)
IL (3) IL265879B2 (es)
MX (2) MX2019004130A (es)
PE (7) PE20191058A1 (es)
PH (6) PH12019550060A1 (es)
SG (3) SG11201903270RA (es)
WO (4) WO2018071054A1 (es)

Families Citing this family (46)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB2526598B (en) * 2014-05-29 2018-11-28 Imagination Tech Ltd Allocation of primitives to primitive blocks
US11574287B2 (en) 2017-10-10 2023-02-07 Text IQ, Inc. Automatic document classification
US11030324B2 (en) * 2017-11-30 2021-06-08 Koninklijke Philips N.V. Proactive resistance to re-identification of genomic data
WO2019191083A1 (en) * 2018-03-26 2019-10-03 Colorado State University Research Foundation Apparatuses, systems and methods for generating and tracking molecular digital signatures to ensure authenticity and integrity of synthetic dna molecules
MX2020012672A (es) * 2018-05-31 2021-02-09 Koninklijke Philips Nv Sistema y metodo para interpretacion de alelos usando un genoma de referencia basado en graficos.
CN108753765B (zh) * 2018-06-08 2020-12-08 中国科学院遗传与发育生物学研究所 一种构建超长连续dna序列的基因组组装方法
US12210904B2 (en) * 2018-06-29 2025-01-28 International Business Machines Corporation Hybridized storage optimization for genomic workloads
US11474978B2 (en) * 2018-07-06 2022-10-18 Capital One Services, Llc Systems and methods for a data search engine based on data profiles
US12300358B2 (en) * 2018-08-20 2025-05-13 The Board Of Trustees Of The Leland Stanford Junior University Systems and methods for compressing genetic sequencing data and uses thereof
GB2585816A (en) * 2018-12-12 2021-01-27 Univ York Proof-of-work for blockchain applications
US20210074381A1 (en) * 2019-09-11 2021-03-11 Enancio Method for the compression of genome sequence data
WO2021063904A1 (en) * 2019-10-01 2021-04-08 Koninklijke Philips N.V. System and methods for the efficient identification and extraction of sequence paths in genome graphs
CN110797087B (zh) * 2019-10-17 2020-11-03 南京医基云医疗数据研究院有限公司 测序序列处理方法及装置、存储介质、电子设备
JP7631330B2 (ja) * 2019-10-18 2025-02-18 コーニンクレッカ フィリップス エヌ ヴェ 多様な表形式データの効果的な圧縮、表現、および展開のためのシステムおよび方法
US12322477B1 (en) * 2019-12-04 2025-06-03 John Hayward Methods of efficiently transforming and comparing recombinable DNA information
US12445148B2 (en) 2020-01-03 2025-10-14 Koninklijke Philips N.V. System and method for effective compression representation and decompression of diverse tabulated data
BR112022015328A2 (pt) * 2020-02-07 2022-09-27 Koninklijke Philips Nv Método e sistema para compressão de informações
CN111243663B (zh) * 2020-02-26 2022-06-07 西安交通大学 一种基于模式增长算法的基因变异检测方法
CN111370070B (zh) * 2020-02-27 2023-10-27 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压缩处理方法
US12014802B2 (en) 2020-03-17 2024-06-18 Western Digital Technologies, Inc. Devices and methods for locating a sample read in a reference genome
US12006539B2 (en) 2020-03-17 2024-06-11 Western Digital Technologies, Inc. Reference-guided genome sequencing
US11837330B2 (en) 2020-03-18 2023-12-05 Western Digital Technologies, Inc. Reference-guided genome sequencing
US12347528B2 (en) 2020-04-07 2025-07-01 Koninklijke Philips N.V. System and method for storing and transporting diverse genomic data
EP3896698A1 (en) * 2020-04-15 2021-10-20 Genomsys SA Method and system for the efficient data compression in mpeg-g
CN111459208A (zh) * 2020-04-17 2020-07-28 南京铁道职业技术学院 针对地铁供电系统电能的操纵系统及其方法
US12224042B2 (en) 2020-06-22 2025-02-11 SanDisk Technologies, Inc. Devices and methods for genome sequencing
US12093803B2 (en) * 2020-07-01 2024-09-17 International Business Machines Corporation Downsampling genomic sequence data
JP2023541341A (ja) * 2020-09-14 2023-10-02 イルミナ インコーポレイテッド 個別化医療のためのカスタムデータファイル
WO2022073810A1 (en) * 2020-10-06 2022-04-14 Koninklijke Philips N.V. Methods and systems for storing genomic data in a file structure comprising protection metadata
AU2021357587A1 (en) * 2020-10-06 2023-06-08 Koninklijke Philips N.V. Methods and systems for storing genomic data in a file structure comprising an information metadata structure
CN112836355B (zh) * 2021-01-14 2023-04-18 西安科技大学 一种预测采煤工作面顶板来压概率的方法
JP7118199B1 (ja) * 2021-03-26 2022-08-15 エヌ・ティ・ティ・コミュニケーションズ株式会社 処理システム、処理方法及び処理プログラム
US12406413B2 (en) 2021-05-10 2025-09-02 Optum Services (Ireland) Limited Predictive data analysis using image representations of genomic data
ES2930699A1 (es) * 2021-06-10 2022-12-20 Veritas Intercontinental S L Metodo de analisis genomico en una plataforma bioinformatica
CN113670643B (zh) * 2021-08-30 2023-05-12 四川虹美智能科技有限公司 智能空调测试方法及系统
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
US20230187020A1 (en) * 2021-12-15 2023-06-15 Illumina Software, Inc. Systems and methods for iterative and scalable population-scale variant analysis
JP2025512716A (ja) 2022-03-08 2025-04-22 イルミナ インコーポレイテッド マルチパスソフトウェアで加速されたゲノムリードマッピングエンジン
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
CN115391284B (zh) * 2022-10-31 2023-02-03 四川大学华西医院 基因数据文件快速识别方法、系统和计算机可读存储介质
WO2024114597A1 (en) * 2022-12-02 2024-06-06 City University Of Hong Kong Reinforcement-learning-based network transmission of compressed genome sequence
CN116541348B (zh) * 2023-03-22 2023-09-26 河北热点科技股份有限公司 数据智能存储方法及终端查询一体机
CN116739646B (zh) * 2023-08-15 2023-11-24 南京易联阳光信息技术股份有限公司 网络交易大数据分析方法及分析系统
CN117153270B (zh) * 2023-10-30 2024-02-02 吉林华瑞基因科技有限公司 一种基因二代测序数据处理方法
CN117708755B (zh) * 2023-12-17 2024-06-21 重庆文理学院 基于生态环境的数据处理方法及装置
WO2025137316A1 (en) * 2023-12-21 2025-06-26 Illumina, Inc. Sequence data processing, retention, and recovery

Family Cites Families (54)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6303297B1 (en) * 1992-07-17 2001-10-16 Incyte Pharmaceuticals, Inc. Database for storage and analysis of full-length sequences
JP3429674B2 (ja) 1998-04-28 2003-07-22 沖電気工業株式会社 多重通信システム
EP1410301A4 (en) * 2000-04-12 2008-01-23 Cleveland Clinic Foundation SYSTEM FOR IDENTIFYING AND ANALYZING GENE EXPRESSION CONTAINING ELEMENTS RICH IN ADENYLATE URIDYLATE (ARE)
FR2820563B1 (fr) * 2001-02-02 2003-05-16 Expway Procede de compression/decompression d'un document structure
US20040153255A1 (en) * 2003-02-03 2004-08-05 Ahn Tae-Jin Apparatus and method for encoding DNA sequence, and computer readable medium
DE10320711A1 (de) * 2003-05-08 2004-12-16 Siemens Ag Verfahren und Anordnung zur Einrichtung und Aktualisierung einer Benutzeroberfläche zum Zugriff auf Informationsseiten in einem Datennetz
US8280640B2 (en) * 2003-08-11 2012-10-02 Eloret Corporation System and method for pattern recognition in sequential data
WO2005094363A2 (en) * 2004-03-30 2005-10-13 New York University System, method and software arrangement for bi-allele haplotype phasing
WO2006052242A1 (en) * 2004-11-08 2006-05-18 Seirad, Inc. Methods and systems for compressing and comparing genomic data
WO2007132461A2 (en) * 2006-05-11 2007-11-22 Ramot At Tel Aviv University Ltd. Classification of protein sequences and uses of classified proteins
SE531398C2 (sv) 2007-02-16 2009-03-24 Scalado Ab Generering av en dataström och identifiering av positioner inuti en dataström
KR101369745B1 (ko) * 2007-04-11 2014-03-07 삼성전자주식회사 비동기화된 비트스트림들의 다중화 및 역다중화 방법 및장치
US8832112B2 (en) * 2008-06-17 2014-09-09 International Business Machines Corporation Encoded matrix index
GB2477703A (en) * 2008-11-14 2011-08-10 Real Time Genomics Inc A method and system for analysing data sequences
US20100217532A1 (en) * 2009-02-25 2010-08-26 University Of Delaware Systems and methods for identifying structurally or functionally significant amino acid sequences
AU2010313247A1 (en) * 2009-10-30 2012-05-24 Synthetic Genomics, Inc. Encoding text into nucleic acid sequences
EP2362657B1 (en) * 2010-02-18 2013-04-24 Research In Motion Limited Parallel entropy coding and decoding methods and devices
WO2011143231A2 (en) * 2010-05-10 2011-11-17 The Broad Institute High throughput paired-end sequencing of large-insert clone libraries
KR101952965B1 (ko) * 2010-05-25 2019-02-27 더 리젠츠 오브 더 유니버시티 오브 캘리포니아 Ｂａｍｂａｍ：고처리율 서열분석 데이터의 병렬 비교 분석
US20140229495A1 (en) * 2011-01-19 2014-08-14 Koninklijke Philips N.V. Method for processing genomic data
US9215162B2 (en) * 2011-03-09 2015-12-15 Annai Systems Inc. Biological data networks and methods therefor
WO2012168815A2 (en) * 2011-06-06 2012-12-13 Koninklijke Philips Electronics N.V. Method for assembly of nucleic acid sequence data
BR112013032332B1 (pt) * 2011-06-16 2022-08-16 Ge Video Compression, Llc Inicialização de contexto em codificação de entropia
US8707289B2 (en) * 2011-07-20 2014-04-22 Google Inc. Multiple application versions
CN104081772B (zh) * 2011-10-06 2018-04-10 弗劳恩霍夫应用研究促进协会 熵编码缓冲器配置
CA2854832C (en) * 2011-11-07 2023-05-23 Ingenuity Systems, Inc. Methods and systems for identification of causal genomic variants
KR101922129B1 (ko) * 2011-12-05 2018-11-26 삼성전자주식회사 차세대 시퀀싱을 이용하여 획득된 유전 정보를 압축 및 압축해제하는 방법 및 장치
US10140683B2 (en) * 2011-12-08 2018-11-27 Five3 Genomics, Llc Distributed system providing dynamic indexing and visualization of genomic data
EP2608096B1 (en) * 2011-12-24 2020-08-05 Tata Consultancy Services Ltd. Compression of genomic data file
US9600625B2 (en) * 2012-04-23 2017-03-21 Bina Technologies, Inc. Systems and methods for processing nucleic acid sequence data
CN103049680B (zh) * 2012-12-29 2016-09-07 深圳先进技术研究院 基因测序数据读取方法及系统
US9679104B2 (en) * 2013-01-17 2017-06-13 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
WO2014145503A2 (en) * 2013-03-15 2014-09-18 Lieber Institute For Brain Development Sequence alignment using divide and conquer maximum oligonucleotide mapping (dcmom), apparatus, system and method related thereto
JP6054790B2 (ja) * 2013-03-28 2016-12-27 三菱スペース・ソフトウエア株式会社 遺伝子情報記憶装置、遺伝子情報検索装置、遺伝子情報記憶プログラム、遺伝子情報検索プログラム、遺伝子情報記憶方法、遺伝子情報検索方法及び遺伝子情報検索システム
GB2512829B (en) * 2013-04-05 2015-05-27 Canon Kk Method and apparatus for encoding or decoding an image with inter layer motion information prediction according to motion information compression scheme
WO2014186604A1 (en) * 2013-05-15 2014-11-20 Edico Genome Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
KR101522087B1 (ko) * 2013-06-19 2015-05-28 삼성에스디에스 주식회사 미스매치를 고려한 염기 서열 정렬 시스템 및 방법
CN103336916B (zh) * 2013-07-05 2016-04-06 中国科学院数学与系统科学研究院 一种测序序列映射方法及系统
US20150032711A1 (en) * 2013-07-06 2015-01-29 Victor Kunin Methods for identification of organisms, assigning reads to organisms, and identification of genes in metagenomic sequences
KR101493982B1 (ko) * 2013-09-26 2015-02-23 대한민국 품종인식 코드화 시스템 및 이를 이용한 코드화 방법
CN104699998A (zh) * 2013-12-06 2015-06-10 国际商业机器公司 用于对基因组进行压缩和解压缩的方法和装置
US10902937B2 (en) * 2014-02-12 2021-01-26 International Business Machines Corporation Lossless compression of DNA sequences
US9639542B2 (en) * 2014-02-14 2017-05-02 Sap Se Dynamic mapping of extensible datasets to relational database schemas
US9886561B2 (en) * 2014-02-19 2018-02-06 The Regents Of The University Of California Efficient encoding and storage and retrieval of genomic data
US9354922B2 (en) 2014-04-02 2016-05-31 International Business Machines Corporation Metadata-driven workflows and integration with genomic data processing systems and techniques
US20150379195A1 (en) * 2014-06-25 2015-12-31 The Board Of Trustees Of The Leland Stanford Junior University Software haplotying of hla loci
GB2527588B (en) * 2014-06-27 2016-05-18 Gurulogic Microsystems Oy Encoder and decoder
US20160019339A1 (en) * 2014-07-06 2016-01-21 Mercator BioLogic Incorporated Bioinformatics tools, systems and methods for sequence assembly
US10230390B2 (en) * 2014-08-29 2019-03-12 Bonnie Berger Leighton Compressively-accelerated read mapping framework for next-generation sequencing
US10116632B2 (en) * 2014-09-12 2018-10-30 New York University System, method and computer-accessible medium for secure and compressed transmission of genomic data
US20160125130A1 (en) * 2014-11-05 2016-05-05 Agilent Technologies, Inc. Method for assigning target-enriched sequence reads to a genomic location
CN107851137A (zh) * 2015-06-16 2018-03-27 汉诺威戈特弗里德威廉莱布尼茨大学 用于压缩基因组数据的方法
CN105956417A (zh) * 2016-05-04 2016-09-21 西安电子科技大学 云环境下基于编辑距离的相似碱基序列查询方法
CN105975811B (zh) * 2016-05-09 2019-03-15 管仁初 一种智能比对的基因序列分析装置

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