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WO2001043051A3 - Computer method and apparatus for revealing promotor motifs - Google Patents

Computer method and apparatus for revealing promotor motifs Download PDF

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Publication number
WO2001043051A3
WO2001043051A3 PCT/US2000/042469 US0042469W WO0143051A3 WO 2001043051 A3 WO2001043051 A3 WO 2001043051A3 US 0042469 W US0042469 W US 0042469W WO 0143051 A3 WO0143051 A3 WO 0143051A3
Authority
WO
WIPO (PCT)
Prior art keywords
repeats
genome
database
motifs
highlighted
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/US2000/042469
Other languages
French (fr)
Other versions
WO2001043051A9 (en
WO2001043051A2 (en
Inventor
Betsey D Dyer
Mark D Leblanc
Glen Aspeslagh
Nathan P Buggia
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.)
BOARD OF TRUSTEES OF WHEATON COLLEGE
TRUSTEES OF WHEATON COLLEGE BO
Original Assignee
BOARD OF TRUSTEES OF WHEATON COLLEGE
TRUSTEES OF WHEATON COLLEGE BO
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 BOARD OF TRUSTEES OF WHEATON COLLEGE, TRUSTEES OF WHEATON COLLEGE BO filed Critical BOARD OF TRUSTEES OF WHEATON COLLEGE
Publication of WO2001043051A2 publication Critical patent/WO2001043051A2/en
Anticipated expiration legal-status Critical
Publication of WO2001043051A9 publication Critical patent/WO2001043051A9/en
Publication of WO2001043051A3 publication Critical patent/WO2001043051A3/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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/30—Data warehousing; Computing architectures
    • 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
    • G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
    • 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

Landscapes

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

Abstract

A computer search tool and supporting database is presented for use in analyzing genomes. The database is formed from a search of inverted and other repeats in a given genome, especially of motifs having such repeats. Indications of found repeats, length, location in the genome sequence and nearest gene are recorded in the database. The computer search tool includes a search engine, browser and drawing member. The search engine responds to user requests for certain repeats (e.g., specified in terms of length and/or subsequence within). The browser enables viewing of a graphical representation (generated by the drawing member) of the genome, with the repeats highlighted. The invention computer search tool enables analysis of the highlighted repeats against known regulatory sites/promotor motifs of other known sequences or relative to each other across the genome.
PCT/US2000/042469 1999-11-30 2000-11-30 Computer method and apparatus for revealing promotor motifs Ceased WO2001043051A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US16805099P 1999-11-30 1999-11-30
US60/168,050 1999-11-30

Publications (3)

Publication Number Publication Date
WO2001043051A2 WO2001043051A2 (en) 2001-06-14
WO2001043051A9 WO2001043051A9 (en) 2002-08-01
WO2001043051A3 true WO2001043051A3 (en) 2002-10-10

Family

ID=22609894

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/042469 Ceased WO2001043051A2 (en) 1999-11-30 2000-11-30 Computer method and apparatus for revealing promotor motifs

Country Status (1)

Country Link
WO (1) WO2001043051A2 (en)

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP6471091B2 (en) 2012-07-06 2019-02-13 ナント ホールディングス アイピー，エルエルシー Healthcare analysis stream management
CN110993033A (en) * 2019-11-14 2020-04-10 北京诺禾致源科技股份有限公司 Genome data processing method, system and device

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
DEVINE S E ET AL: "A transposon-based strategy for sequencing repetitive DNA in eucaryotic genomes", GENOME RESEARCH, COLD SPRING HARBOR LABORATORY PRESS, US, vol. 7, 1997, pages 551 - 563, XP002145187, ISSN: 1088-9051 *
LEBLANC, M.; APESLAGH, G.; BUGGIA N.; DYER, B.: "An annotated catalog of inverted repeats of Caenorhabditis elegans chromosomes III and X, with observations concerning odd/even biases and conserved motifs", GENOME RESEARCH, September 2000 (2000-09-01), US, pages 1381 - 1392, XP002194627, ISSN: 1088-9051 *
QUENTIN, Y.; FICHANT, G.: "Fast identification of repetitive elements in biological sequences", JOURNAL OF THEORETICAL BIOLOGY, vol. 166, no. 1, 7 January 1994 (1994-01-07), UK, pages 51 - 61, XP001066371, ISSN: 0022-5193 *

Also Published As

Publication number Publication date
WO2001043051A9 (en) 2002-08-01
WO2001043051A2 (en) 2001-06-14

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