WO2001063543A8 - Procede et systeme d'assemblage d'un genome entier au moyen d'un ensemble de donnees prises au hasard - Google Patents

Procede et systeme d'assemblage d'un genome entier au moyen d'un ensemble de donnees prises au hasard

Info

Publication number
WO2001063543A8
WO2001063543A8 PCT/US2001/002704 US0102704W WO0163543A8 WO 2001063543 A8 WO2001063543 A8 WO 2001063543A8 US 0102704 W US0102704 W US 0102704W WO 0163543 A8 WO0163543 A8 WO 0163543A8
Authority
WO
WIPO (PCT)
Prior art keywords
shot
genome
assembly
dna
data set
Prior art date
Application number
PCT/US2001/002704
Other languages
English (en)
Other versions
WO2001063543A3 (fr
WO2001063543A2 (fr
Inventor
Gene W Myers
Arthur L Delcher
Ian M Dew
Michael J Flanigan
Saul A Kravitz
Clark M Mobarry
Knut Reinert
Karin A Remington
Granger G Sutton
Original Assignee
Pe Corp Ny
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 US09/526,131 external-priority patent/US6714874B1/en
Application filed by Pe Corp Ny filed Critical Pe Corp Ny
Priority to JP2001562433A priority Critical patent/JP2003530631A/ja
Priority to EP01908713A priority patent/EP1285390A2/fr
Priority to AU2001236555A priority patent/AU2001236555A1/en
Priority to CA002400890A priority patent/CA2400890A1/fr
Publication of WO2001063543A2 publication Critical patent/WO2001063543A2/fr
Publication of WO2001063543A8 publication Critical patent/WO2001063543A8/fr
Publication of WO2001063543A3 publication Critical patent/WO2001063543A3/fr

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
    • 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

Landscapes

  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Investigating Or Analysing Biological Materials (AREA)

Abstract

La présente invention concerne des procédés et des systèmes d'assemblage d'un génome à partir d'un ensemble pris au hasard de fragments d'ADN à extrémité séquentielle. Plus particulièrement, la présente invention concerne un procédé destiné à déterminer la séquence génomique (séquence de base et orientation) d'un génome complexe au moyen d'informations d'ADN en séquence générées à partir de plusieurs fragments d'ADN obtenus par le génome. Ce procédé est particulièrement utile dans l'assemblage de génomes d'au moins 10MB (jusqu'à 5GB) et qui sont constitués d'au moins 5 % de séquences d'ADN répétitif (jusqu'à 25%), mais il peut également être utilisé pour de plus petits génomes avec un pourcentage inférieur d'ADN répétitif.
PCT/US2001/002704 2000-02-22 2001-01-29 Procede et systeme d'assemblage d'un genome entier au moyen d'un ensemble de donnees prises au hasard WO2001063543A2 (fr)

Priority Applications (4)

Application Number Priority Date Filing Date Title
JP2001562433A JP2003530631A (ja) 2000-02-22 2001-01-29 ショットガンデータ集合を用いた全ゲノムのアセンブリのための方法及びシステム
EP01908713A EP1285390A2 (fr) 2000-02-22 2001-01-29 Procede et systeme d'assemblage d'un genome entier au moyen d'un ensemble de donnees prises au hasard
AU2001236555A AU2001236555A1 (en) 2000-02-22 2001-01-29 Method and system for the assembly of a whole genome using a shot-gun data set
CA002400890A CA2400890A1 (fr) 2000-02-22 2001-01-29 Procede et systeme d'assemblage d'un genome entier au moyen d'un ensemble de donnees prises au hasard

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US18375800P 2000-02-22 2000-02-22
US60/183,758 2000-02-22
US09/526,131 2000-03-15
US09/526,131 US6714874B1 (en) 2000-03-15 2000-03-15 Method and system for the assembly of a whole genome using a shot-gun data set

Publications (3)

Publication Number Publication Date
WO2001063543A2 WO2001063543A2 (fr) 2001-08-30
WO2001063543A8 true WO2001063543A8 (fr) 2002-02-07
WO2001063543A3 WO2001063543A3 (fr) 2002-12-05

Family

ID=26879491

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/002704 WO2001063543A2 (fr) 2000-02-22 2001-01-29 Procede et systeme d'assemblage d'un genome entier au moyen d'un ensemble de donnees prises au hasard

Country Status (5)

Country Link
EP (1) EP1285390A2 (fr)
JP (1) JP2003530631A (fr)
AU (1) AU2001236555A1 (fr)
CA (1) CA2400890A1 (fr)
WO (1) WO2001063543A2 (fr)

Families Citing this family (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2003330934A (ja) * 2002-05-10 2003-11-21 Celestar Lexico-Sciences Inc 変異体配列解析装置、変異体配列解析方法、プログラム、および、記録媒体
US7575865B2 (en) * 2003-01-29 2009-08-18 454 Life Sciences Corporation Methods of amplifying and sequencing nucleic acids
US20110004616A1 (en) * 2007-10-31 2011-01-06 National Institute Of Agrobiological Sciences Base sequence determination program, base sequence determination device, and base sequence determination method
CN101504697B (zh) * 2008-12-12 2010-09-08 深圳华大基因研究院 一种片段连接支架的构建方法和系统
CN101457253B (zh) * 2008-12-12 2011-08-31 深圳华大基因研究院 一种测序序列纠错方法、系统及设备
US20120197533A1 (en) * 2010-10-11 2012-08-02 Complete Genomics, Inc. Identifying rearrangements in a sequenced genome
TWI420007B (zh) * 2011-03-04 2013-12-21 Hsueh Ting Chu 基因測序序列的組合系統及方法
WO2012171213A1 (fr) * 2011-06-17 2012-12-20 深圳华大基因科技有限公司 Procédé et système pour l'assemblage d'un génome
BR102012031096B1 (pt) * 2012-12-05 2019-10-22 Empresa Brasileira De Pesquisa Agropecuaria Embrapa método e uso para verificação de erros de montagem em genomas
AU2013382195B2 (en) 2013-03-13 2019-09-19 Illumina, Inc. Methods and systems for aligning repetitive DNA elements
CN104164479B (zh) * 2014-04-04 2017-09-19 深圳华大基因科技服务有限公司 杂合基因组处理方法
CN104298892B (zh) * 2014-09-18 2017-05-10 天津诺禾致源生物信息科技有限公司 基因融合的检测装置和方法

Also Published As

Publication number Publication date
AU2001236555A1 (en) 2001-09-03
JP2003530631A (ja) 2003-10-14
WO2001063543A3 (fr) 2002-12-05
CA2400890A1 (fr) 2001-08-30
EP1285390A2 (fr) 2003-02-26
WO2001063543A2 (fr) 2001-08-30

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