CN114930724A - 创建基因突变词典及利用基因突变词典压缩基因组数据的方法和装置 - Google Patents

创建基因突变词典及利用基因突变词典压缩基因组数据的方法和装置 Download PDF

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Publication number
CN114930724A
CN114930724A CN201980102589.7A CN201980102589A CN114930724A CN 114930724 A CN114930724 A CN 114930724A CN 201980102589 A CN201980102589 A CN 201980102589A CN 114930724 A CN114930724 A CN 114930724A
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data
dictionary
mutant
mutation
genome
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CN201980102589.7A
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徐崇钧
周玉君
邓梓晴
龚梅花
蒋慧
徐讯
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MGI Tech Co Ltd
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MGI Tech Co Ltd
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Publication of CN114930724A publication Critical patent/CN114930724A/zh
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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
    • H03M7/40—Conversion to or from variable length codes, e.g. Shannon-Fano code, Huffman code, Morse code
    • H03M7/4031—Fixed length to variable length coding
    • H03M7/4037—Prefix coding
    • H03M7/4043—Adaptive prefix coding
    • 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
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • H03M7/70—Type of the data to be coded, other than image and sound

Abstract

一种创建基因突变词典的方法及利用基因突变词典压缩基因组数据的方法和装置，其中创建基因突变词典的方法包括：获取一种物种的多个个体的基因组序列数据和该物种的参考基因组数据；将多个个体的基因组序列数据分别比对到参考基因组数据上，得到每个个体的基因组序列数据相对于参考基因组数据的突变结果；将该物种的基因组划分成若干个有生物学意义的单元分区；根据突变结果，对每个单元分区的突变体情况分别进行统计，生成每个单元分区在多个个体中的全部突变体类型，并对突变体类型编号获得基因突变词典。本发明解决了基因组数据压缩的难题，使其存储量明显降低，并极大地降低了存储数据的成本。

Description

PCT国内申请，说明书已公开。

Claims (16)

  1. PCT国内申请，权利要求书已公开。
CN201980102589.7A 2019-12-31 2019-12-31 创建基因突变词典及利用基因突变词典压缩基因组数据的方法和装置 Pending CN114930724A (zh)

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US (1) US20220383987A1 (zh)
EP (1) EP4087139A4 (zh)
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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN116246715A (zh) * 2023-04-27 2023-06-09 倍科为(天津)生物技术有限公司 多样本基因突变数据存储方法、装置、设备及介质
WO2024077568A1 (zh) * 2022-10-13 2024-04-18 深圳华大智造科技股份有限公司 参考序列的构建方法、宏基因组数据压缩方法和电子设备

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JP2003188735A (ja) * 2001-12-13 2003-07-04 Ntt Data Corp データ圧縮装置及び方法並びにプログラム
US20040153255A1 (en) * 2003-02-03 2004-08-05 Ahn Tae-Jin Apparatus and method for encoding DNA sequence, and computer readable medium
EP2612271A4 (en) * 2010-08-31 2017-07-19 Annai Systems Inc. Method and systems for processing polymeric sequence data and related information
US8937564B2 (en) * 2013-01-10 2015-01-20 Infinidat Ltd. System, method and non-transitory computer readable medium for compressing genetic information
CN103546162B (zh) * 2013-09-22 2016-08-17 上海交通大学 基于非连续上下文建模和最大熵原则的基因压缩方法
JP6198659B2 (ja) * 2014-04-03 2017-09-20 株式会社日立ハイテクノロジーズ 配列データ解析装置、ｄｎａ解析システムおよび配列データ解析方法
CA3191504A1 (en) * 2014-05-30 2015-12-03 Sequenom, Inc. Chromosome representation determinations
KR101832373B1 (ko) * 2015-08-28 2018-02-26 주식회사 케이티 유전 변이 정보 축소 및 전달 장치와 그 방법
CN110914911B (zh) * 2017-05-16 2023-09-22 生命科技股份有限公司 压缩分子标记的核酸序列数据的方法
CN109450452B (zh) * 2018-11-27 2020-07-10 中国科学院计算技术研究所 一种针对基因数据的取样字典树索引的压缩方法和系统

Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2024077568A1 (zh) * 2022-10-13 2024-04-18 深圳华大智造科技股份有限公司 参考序列的构建方法、宏基因组数据压缩方法和电子设备
CN116246715A (zh) * 2023-04-27 2023-06-09 倍科为(天津)生物技术有限公司 多样本基因突变数据存储方法、装置、设备及介质
CN116246715B (zh) * 2023-04-27 2024-04-16 倍科为(天津)生物技术有限公司 多样本基因突变数据存储方法、装置、设备及介质

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US20220383987A1 (en) 2022-12-01
EP4087139A1 (en) 2022-11-09
EP4087139A4 (en) 2023-01-18

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