WO2009017023A1 - 核酸の塩基配列及び塩基修飾を解析する装置、方法及びプログラム - Google Patents

核酸の塩基配列及び塩基修飾を解析する装置、方法及びプログラム Download PDF

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Publication number
WO2009017023A1
WO2009017023A1 PCT/JP2008/063277 JP2008063277W WO2009017023A1 WO 2009017023 A1 WO2009017023 A1 WO 2009017023A1 JP 2008063277 W JP2008063277 W JP 2008063277W WO 2009017023 A1 WO2009017023 A1 WO 2009017023A1
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WO
WIPO (PCT)
Prior art keywords
base composition
nucleic acid
base
partial
processing unit
Prior art date
Application number
PCT/JP2008/063277
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English (en)
French (fr)
Inventor
Tsutomu Suzuki
Hiroki Ueda
Original Assignee
The University Of Tokyo
Japan Biological Informatics Consortium
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 The University Of Tokyo, Japan Biological Informatics Consortium filed Critical The University Of Tokyo
Priority to US12/452,859 priority Critical patent/US20100262376A1/en
Priority to EP08791529A priority patent/EP2175266A1/en
Publication of WO2009017023A1 publication Critical patent/WO2009017023A1/ja

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Other Investigation Or Analysis Of Materials By Electrical Means (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

　核酸の解析を迅速且つ正確に行うことのできる装置を提供する。　 　核酸の全体塩基組成に基づいて複数の塩基組成セットを作成するとともに、塩基組成セットが末端位置の部分塩基組成の塩基数の昇順に階層化された階層構造を作成し、塩基組成セットとその末端位置の部分塩基組成に塩基を１つ追加した部分塩基組成を末端位置に有する他の塩基組成セットとの間に接続関係を作成する処理部と、部分塩基組成について、対応したプロダクトイオンの予測される質量値を算出し、予測される質量値と核酸由来のプロダクトイオンの実際に得られた質量値との比較に基づいて塩基組成セットに重みを付与する処理部と、塩基組成セットに付与された重みに基づいて階層構造の最外階層から接続関係を辿りながら、各階層に属する塩基組成セットのうち１つを選択することによって、核酸の末端塩基から塩基配列を順次決定する処理部と、を含む核酸解析装置とする。
PCT/JP2008/063277 2007-07-27 2008-07-24 核酸の塩基配列及び塩基修飾を解析する装置、方法及びプログラム WO2009017023A1 (ja)

Priority Applications (2)

Application Number Priority Date Filing Date Title
US12/452,859 US20100262376A1 (en) 2007-07-27 2008-07-24 Apparatus, method and program for analyzing nucleic acid base sequence and base modification
EP08791529A EP2175266A1 (en) 2007-07-27 2008-07-24 Apparatus, process and program for analyzing nucleic acid base sequence and base modification

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
JP2007-195555 2007-07-27
JP2007195555A JP2009031128A (ja) 2007-07-27 2007-07-27 核酸の塩基配列及び塩基修飾を解析する装置、方法及びプログラム

Publications (1)

Publication Number Publication Date
WO2009017023A1 true WO2009017023A1 (ja) 2009-02-05

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/JP2008/063277 WO2009017023A1 (ja) 2007-07-27 2008-07-24 核酸の塩基配列及び塩基修飾を解析する装置、方法及びプログラム

Country Status (4)

Country Link
US (1) US20100262376A1 (ja)
EP (1) EP2175266A1 (ja)
JP (1) JP2009031128A (ja)
WO (1) WO2009017023A1 (ja)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2462244A2 (en) * 2009-08-06 2012-06-13 Ibis Biosciences, Inc. Non-mass determined base compositions for nucleic acid detection

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3802818A4 (en) * 2018-05-25 2022-03-02 New York Institute of Technology METHOD AND SYSTEM FOR USE IN DIRECT RNA SEQUENCING

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2005503570A (ja) * 2001-09-14 2005-02-03 エフ．ホフマン−ラ　ロシュ　アーゲー 核酸の配列決定方法

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2005503570A (ja) * 2001-09-14 2005-02-03 エフ．ホフマン−ラ　ロシュ　アーゲー 核酸の配列決定方法

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
HERBERT OBERACHER ET AL.: "Automated de novo sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry", JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, vol. 15, no. Issue 1, January 2004 (2004-01-01), pages 32 - 42, XP004482442 *
JINSONG NI ET AL.: "Interpretation of Oligonucleotide Mass Spectra for Determination of Sequence Using ElectrosprayIonization and Tandem Mass Spectrometry", ANALYTICAL CHEMISTRY, vol. 68, no. 13, pages 1989 - 1999, XP002263308 *
OBERACHER H.; MAYR B. M.; HUBER C. G., JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, vol. 15, no. 1, 2004, pages 32 - 42

Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2462244A2 (en) * 2009-08-06 2012-06-13 Ibis Biosciences, Inc. Non-mass determined base compositions for nucleic acid detection
US9080209B2 (en) 2009-08-06 2015-07-14 Ibis Biosciences, Inc. Non-mass determined base compositions for nucleic acid detection
EP2462244B1 (en) * 2009-08-06 2016-07-20 Ibis Biosciences, Inc. Non-mass determined base compositions for nucleic acid detection

Also Published As

Publication number Publication date
US20100262376A1 (en) 2010-10-14
JP2009031128A (ja) 2009-02-12
EP2175266A1 (en) 2010-04-14

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