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WO2001063543A8 - Method and system for the assembly of a whole genome using a shot-gun data set - Google Patents

Method and system for the assembly of a whole genome using a shot-gun data set

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
Legal status (The legal status 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 status listed.)
Ceased
Application number
PCT/US2001/002704
Other languages
French (fr)
Other versions
WO2001063543A3 (en
WO2001063543A2 (en
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
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Applied Biosystems Inc
Original Assignee
PE Corp
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 filed Critical PE Corp
Priority to JP2001562433A priority Critical patent/JP2003530631A/en
Priority to EP01908713A priority patent/EP1285390A2/en
Priority to CA002400890A priority patent/CA2400890A1/en
Priority to AU2001236555A priority patent/AU2001236555A1/en
Publication of WO2001063543A2 publication Critical patent/WO2001063543A2/en
Publication of WO2001063543A8 publication Critical patent/WO2001063543A8/en
Anticipated expiration legal-status Critical
Publication of WO2001063543A3 publication Critical patent/WO2001063543A3/en
Ceased legal-status Critical Current

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)
  • Bioinformatics & Cheminformatics (AREA)
  • Evolutionary Biology (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Analytical Chemistry (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

The present invention provides methods and systems for assembling a genome from a shot-gun set of end sequenced DNA fragments. Specifically, the present invention provides a method of determining the genomic sequence (base sequence and orientation) of a complex genome using DNA sequence information generated from a collection of DNA fragments obtained from the genome. The present method is particularly useful in assembling genomes of at least 10MB (up to 5GB) and which are made up of at least 5% repetitive DNA sequences (up to 25% repetitive), but can be used also for smaller genomes with a lower percentage of repetitive DNA.
PCT/US2001/002704 2000-02-22 2001-01-29 Method and system for the assembly of a whole genome using a shot-gun data set Ceased WO2001063543A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
JP2001562433A JP2003530631A (en) 2000-02-22 2001-01-29 Methods and systems for whole genome assembly using shotgun data sets
EP01908713A EP1285390A2 (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 (en) 2000-02-22 2001-01-29 Method and system for the assembly of a whole genome using a shot-gun data set
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

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 US6714874B1 (en) 2000-03-15 2000-03-15 Method and system for the assembly of a whole genome using a shot-gun data set
US09/526,131 2000-03-15

Publications (3)

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

Family

ID=26879491

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/002704 Ceased WO2001063543A2 (en) 2000-02-22 2001-01-29 Method and system for the assembly of a whole genome using a shot-gun data set

Country Status (5)

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

Families Citing this family (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2003330934A (en) * 2002-05-10 2003-11-21 Celestar Lexico-Sciences Inc Variant sequence analyzer, variant sequence analysis method, program, and recording medium
US7575865B2 (en) * 2003-01-29 2009-08-18 454 Life Sciences Corporation Methods of amplifying and sequencing nucleic acids
JP5288355B2 (en) * 2007-10-31 2013-09-11 独立行政法人農業生物資源研究所 Base sequence determination program, base sequence determination device, and base sequence determination method
CN101504697B (en) * 2008-12-12 2010-09-08 深圳华大基因研究院 A method and system for constructing fragment-connected scaffolds
CN101457253B (en) * 2008-12-12 2011-08-31 深圳华大基因研究院 Sequencing sequence error correction method, system and device
US20120197533A1 (en) * 2010-10-11 2012-08-02 Complete Genomics, Inc. Identifying rearrangements in a sequenced genome
TWI420007B (en) * 2011-03-04 2013-12-21 Hsueh Ting Chu System and method of assembling dna reads
WO2012171213A1 (en) * 2011-06-17 2012-12-20 深圳华大基因科技有限公司 Method and system for assembly of genome
BR102012031096B1 (en) * 2012-12-05 2019-10-22 Empresa Brasileira De Pesquisa Agropecuaria Embrapa method and use for verifying assembly errors in genomes
AU2013382195B2 (en) 2013-03-13 2019-09-19 Illumina, Inc. Methods and systems for aligning repetitive DNA elements
CN104164479B (en) * 2014-04-04 2017-09-19 深圳华大基因科技服务有限公司 Heterozygous genome processing method
CN104298892B (en) * 2014-09-18 2017-05-10 天津诺禾致源生物信息科技有限公司 Detection device and method for gene fusion
CN117352060A (en) * 2023-11-16 2024-01-05 云南省烟草农业科学研究院 Method for assembling chromosome-level genome of heterotetraploid tobacco

Also Published As

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

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