[go: up one dir, main page]

WO2004005547A3 - Method for identifying hypersensitive site consensus sequences - Google Patents

Method for identifying hypersensitive site consensus sequences Download PDF

Info

Publication number
WO2004005547A3
WO2004005547A3 PCT/GB2003/002895 GB0302895W WO2004005547A3 WO 2004005547 A3 WO2004005547 A3 WO 2004005547A3 GB 0302895 W GB0302895 W GB 0302895W WO 2004005547 A3 WO2004005547 A3 WO 2004005547A3
Authority
WO
WIPO (PCT)
Prior art keywords
identifying
consensus sequences
hypersensitive site
site consensus
sequences
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/GB2003/002895
Other languages
French (fr)
Other versions
WO2004005547A2 (en
Inventor
Robert Otto Johannes Weinzierl
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.)
Ip2ipo Innovations Ltd
Original Assignee
Imperial College Innovations Ltd
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 GB0215547A external-priority patent/GB0215547D0/en
Priority claimed from PCT/GB2002/003080 external-priority patent/WO2003004702A2/en
Application filed by Imperial College Innovations Ltd filed Critical Imperial College Innovations Ltd
Priority to AU2003281288A priority Critical patent/AU2003281288A1/en
Publication of WO2004005547A2 publication Critical patent/WO2004005547A2/en
Publication of WO2004005547A3 publication Critical patent/WO2004005547A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

Links

Classifications

    • 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
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • 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

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • General Chemical & Material Sciences (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Genetics & Genomics (AREA)
  • Medicinal Chemistry (AREA)
  • Veterinary Medicine (AREA)
  • Public Health (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Animal Behavior & Ethology (AREA)
  • Traffic Control Systems (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The present invention relates to a method for identifying one or more HS consensus sequences comprising the steps of: (a) providing a plurality of HS core sequences; (b) using a search algorithm to search for a plurality of motifs that are shared by HS core sequences; and returning one or more HS consensus sequences comprising a plurality of motifs identified in step (b).
PCT/GB2003/002895 2002-07-04 2003-07-04 Method for identifying hypersensitive site consensus sequences Ceased WO2004005547A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2003281288A AU2003281288A1 (en) 2002-07-04 2003-07-04 Method for identifying hypersensitive site consensus sequences

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
GB0215547A GB0215547D0 (en) 2002-07-04 2002-07-04 Method
GB0215547.1 2002-07-04
PCT/GB2002/003080 WO2003004702A2 (en) 2001-07-05 2002-07-04 Method for determining chromatin structure
GBPCT/GB02/003080 2002-07-04

Publications (2)

Publication Number Publication Date
WO2004005547A2 WO2004005547A2 (en) 2004-01-15
WO2004005547A3 true WO2004005547A3 (en) 2004-03-25

Family

ID=30117081

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/GB2003/002895 Ceased WO2004005547A2 (en) 2002-07-04 2003-07-04 Method for identifying hypersensitive site consensus sequences

Country Status (2)

Country Link
AU (1) AU2003281288A1 (en)
WO (1) WO2004005547A2 (en)

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2004286261B2 (en) * 2003-10-27 2010-06-24 Merck Sharp & Dohme Llc Method of designing siRNAs for gene silencing

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2003004702A2 (en) * 2001-07-05 2003-01-16 Imperial College Innovations Limited Method for determining chromatin structure

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2003004702A2 (en) * 2001-07-05 2003-01-16 Imperial College Innovations Limited Method for determining chromatin structure

Non-Patent Citations (11)

* Cited by examiner, † Cited by third party
Title
FRECH K ET AL: "Finding protein-binding sites in DNA sequences: the next generation", TIBS TRENDS IN BIOCHEMICAL SCIENCES, ELSEVIER PUBLICATION, CAMBRIDGE, EN, vol. 22, no. 3, 1 March 1997 (1997-03-01), pages 103 - 104, XP004055069, ISSN: 0968-0004 *
FRISCH MATTHIAS ET AL: "In silico prediction of scaffold/matrix attachment regions in large genomic sequences", GENOME RESEARCH, vol. 12, no. 2, February 2002 (2002-02-01), pages 349 - 354, XP002257587, ISSN: 1088-9051 *
FRITH MARTIN C ET AL: "Detection of cis-element clusters in higher eukaryotic DNA", BIOINFORMATICS (OXFORD), vol. 17, no. 10, October 2001 (2001-10-01), pages 878 - 889, XP002257591, ISSN: 1367-4803 *
FRITH MARTIN C ET AL: "Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences", NUCLEIC ACIDS RESEARCH, vol. 30, no. 14, 15 July 2002 (2002-07-15), pages 3214 - 3224, XP002257592, ISSN: 0305-1048 *
GROSS D S ET AL: "NUCLEASE HYPERSENSITIVE SITES IN CHROMATIN", ANNUAL REVIEW OF BIOCHEMISTRY, PALTO ALTO, CA, US, vol. 57, 1988, pages 159 - 197, XP000879087, ISSN: 0066-4154 *
PFEIFER G P ET AL: "CHROMATIN STRUCTURE ANALYSIS BY LIGATION-MEDIATED AND TERMINAL TRANSFERASE-MEDIATED POLYMERASE CHAIN REACTION", METHODS IN ENZYMOLOGY, ACADEMIC PRESS INC, SAN DIEGO, CA, US, vol. 304, 1999, pages 548 - 571, XP001147579, ISSN: 0076-6879 *
SCHOLZ HOLGER ET AL: "A far upstream cis-element is required for Wilms' tumor-1 (WT1) gene expression in renal cell culture", JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 272, no. 52, 26 December 1997 (1997-12-26), pages 32836 - 32846, XP002257540, ISSN: 0021-9258 *
SMITH C L ET AL: "STRATEGIES FOR MAPPING AND CLONING MACROREGIONS OF MAMMALIAN GENOMES", METHODS IN ENZYMOLOGY, ACADEMIC PRESS INC, SAN DIEGO, CA, US, vol. 151, 1987, pages 461 - 489, XP001147570, ISSN: 0076-6879 *
THIJS GERT ET AL: "A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling", BIOINFORMATICS (OXFORD), vol. 17, no. 12, December 2001 (2001-12-01), pages 1113 - 1122, XP002257589, ISSN: 1367-4803 *
WU THOMAS D ET AL: "Fast probabilistic analysis of sequence function using scoring matrices", BIOINFORMATICS (OXFORD), vol. 16, no. 3, March 2000 (2000-03-01), pages 233 - 244, XP002257590, ISSN: 1367-4803 *
YADA TETSUSHI ET AL: "Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences", BIOINFORMATICS (OXFORD), vol. 14, no. 4, 1998, pages 317 - 325, XP002257588, ISSN: 1367-4803 *

Also Published As

Publication number Publication date
WO2004005547A2 (en) 2004-01-15
AU2003281288A8 (en) 2004-01-23
AU2003281288A1 (en) 2004-01-23

Similar Documents

Publication Publication Date Title
DE10307504A8 (en) Organic electroluminescent component and method for its production
AU2003273180A1 (en) Method of treating actinic keratosis
DE60334570D1 (en) METHOD FOR PRODUCING METAL NANOTEHICLES
GB0301940D0 (en) Cushioning system for footwear and related method of manufacture
NO20031581D0 (en) Method and system for authenticating components of a graphics system
DE60209880D1 (en) HIGH TITANIUM ALLOY AND METHOD FOR THE PRODUCTION THEREOF
TWI348514B (en) Substrate for artificial leathers, artificial leathers and production method of substrate for artificial leathers
GB2424236B (en) Expansion method
IL164496A0 (en) Method of inhibiting restenosis
DE50114793D1 (en) METHOD FOR MILLING TANNING TREE NUTS
NO20043705L (en) Lining run system and method
DE60327601D1 (en) SUPERCONDUCTIVE LAYER AND METHOD FOR THEIR PRODUCTION
AU2003902235A0 (en) Method and system for distributed syndicate gaming
ZA200301390B (en) Method of enhancing skin lightening.
IS7069A (en) Method of producing zaleplon
WO2004005547A3 (en) Method for identifying hypersensitive site consensus sequences
NO20051605L (en) Repair of DNA mutagenic damage
AU2003218188A1 (en) Method of treating onychomycosis
NO20051096D0 (en) Horizontal tree overhaul system and method
AU2003234921A1 (en) Method of knitting knit-wear
ATE382621T1 (en) METHOD FOR PRODUCING NEVIRAPINE
DE50205310D1 (en) ISOFLAVON CONCENTRATES AND METHOD OF MANUFACTURING THEM
WO2002081415A3 (en) Method for inhibiting metap2
AU2003292680A1 (en) Method of selecting novel immunosuppressant
FI20010892L (en) Method for producing xylitol

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CO CR CU CZ DE DK DM DZ EC EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NI NO NZ OM PG PH PL PT RO RU SC SD SE SG SK SL SY TJ TM TN TR TT TZ UA UG US UZ VC VN YU ZA ZM ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZM ZW AM AZ BY KG KZ MD RU TJ TM AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HU IE IT LU MC NL PT RO SE SI SK TR BF BJ CF CG CI CM GA GN GQ GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
122 Ep: pct application non-entry in european phase
NENP Non-entry into the national phase

Ref country code: JP

WWW Wipo information: withdrawn in national office

Country of ref document: JP