Work Files Saved Searches
   My Account                                                  Search:   Quick/Number   Boolean   Advanced   Derwent    Help   


 The Delphion Integrated View

  Buy Now:   Buy PDF- 432pp  PDF  |   File History  |   Other choices   
  Tools:  Citation Link  |  Add to Work File:    
  View:  Expand Details   |  INPADOC   |  Jump to: 
  Go to:  Derwent  
 Email this to a friend  Email this to a friend 
       
Title: US5867402: Computational analysis of nucleic acid information defines binding sites
[ Derwent Title ]


Country: US United States of America

View Images High
Resolution

 Low
 Resolution

 
432 pages

 
Inventor: Schneider, Thomas D.; Frederick, MD
Rogan, Peter K.; Lebanon, PA

Assignee: The United States of America as represented by the Department of Health and Human Services, Washington, DC
other patents from UNITED STATES OF AMERICA, HEALTH & HUMAN SERVICES (597315) (approx. 1,967)
 News, Profiles, Stocks and More about this company

Published / Filed: 1999-02-02 / 1995-06-23

Application Number: US1995000494115

IPC Code: Advanced: C12Q 1/68; G06F 19/00; G06T 7/00;
Core: more...
IPC-7: G06F 17/16;

ECLA Code: G06T7/00B2; C12Q1/68; C12Q1/68B6; G06F19/00C1;

U.S. Class: Current: 702/020; 703/002;
Original: 364/496; 364/578;

Field of Search: 364/496-500,578 395/144 434/279

Priority Number:
1995-06-23  US1995000494115

Abstract:     In accordance with the present invention, binding sites are defined based upon the individual information content of a particular site of interest. Substitutions within the binding site sequences can be analyzed to determine whether the substitution will cause a deleterious mutation or a benign polymorphism. In addition, new binding sites can be identified using individual information content. Further a computer system is described for determining and displaying individual information content of a binding site sequence.

Attorney, Agent or Firm: Morgan & Finnegan, L.L.P. ;

Primary / Asst. Examiners: Ramirez, Ellis B.; Kemper, M.

INPADOC Legal Status: Show legal status actions          Buy Now: Family Legal Status Report

Designated Country: AL AM AP AT AZ BB BG BR BY CA CH CN CZ DE DK EE EP ES FI GB GE HU IL IS JP KE KG KP KR KZ LK LR LS LT LU LV MD MG MK 

Family: Show 3 known family members

First Claim:
Show all 57 claims
We claim:     1. A method of determining sequence conservation of a binding site on a test nucleic acid sequence using a set of sequences, said set including nucleic acid base identity, base position and alignment information, comprising:
  • (a) extracting base identity and alignment information to generate an aligned set of sequences corresponding to at least one pre-determined criterion;
  • (b) generating in a computer an information weight matrix for said extracted information to provide an information model for said nucleic acid sequences, said matrix being calculated in accordance with the formula:
    • Ri (b,l)=2-(-log2 f(b,l)+e(n(l)), where .function.(b,l) is the frequency of each base b at position l in the aligned sequences and e(n(l)) is a sample size correction factor for the n sequences in .function.(b,l);
  • (c) applying in a computer the individual information weight matrix Ri to the test sequence, thereby assigning each position within the test sequence an information-based numerical value; and
  • (d) determining the sequence conservation of the binding site on the test sequence by adding together the information-based numerical values.


Background / Summary: Show background / summary

Drawing Descriptions: Show drawing descriptions

Description: Show description

Forward References: Show 7 U.S. patent(s) that reference this one

       
U.S. References: Go to Result Set: All U.S. references   |  Forward references (7)   |   Backward references (0)   |   Citation Link

       
Foreign References: None

Other Abstract Info: CHEMABS 126(12)153652J DERABS C1997-087530

Other References:
  • Stephens et al., "Features of Spliceosome Evolution and Function Inferred from Analysis of the Information at Human Splice Sites", Journal of Medical Biology, 1992, vol. 228, pp. 1124-1136. (13 pages) [ISI abstract]
  • Schneider et al., "Sequence logos: a new way to display consensus sequences", Nucleic Acids Research, 1990, vol. 18, pp. 6097-6100. (4 pages) Cited by 4 patents
  • Staden, R., "Computer methods to locate signals in nucleic acid sequences", Nucleic Acids Research, 1984, vol. 12, pp. 505-519. (15 pages)
  • Schnider, T. "Poster on Information Theory and Individual Information," Web page at http://www-lmmb.ncifcrf.gov/~toms/just.say.no/index.html, Feb. 27, 1996--updated Oct. 18, 1996.
  • Thomas D. Schneider, "Sequence Logos, Machine/Channel Capacity, Maxwell's Demon, and Molecular Computers: A Review of the Theory of Molecular Machines," Nanotechnology vol. 5, pp. 1-8, 1994. (18 pages) Cited by 2 patents [ISI abstract]
  • Nathan D. Herman, et al., "High Information Conservation Implies that at Least Three Proteins Bind Independently to F Plasmid incD Repeats," Journal of Bacteriology, pp. 3558-3560, Jun. 1992. (3 pages) [ISI abstract]
  • Thomas D. Schneider, et al., "Sequence Logos: A New Way to Display Consensus Sequences," Nucleic Acids Research, vol. 18, No. 20, pp. 6097-6100, Sep. 12, 1990. (4 pages) Cited by 4 patents
  • Otto G. Berg, et al., "Selection of DNA Binding Sites by Regulatory Proteins: The Binding Specificity of Cyclic AMP Receptor Protein to Recognition Sites," Journal of Molecular Biology, No. vol. 200, No. 4, pp. 709-723, 1988. (15 pages)
  • Otto G. Berg, "Selection of DNA Binding Sites by Regulatory Proteins: The LexA Protein and the Arginine Repressor Use Different Strategies for Functional Specificity," Nucleic Acids Research, vol. 16, No. 11, pp. 5089-5105, Apr. 26, 1988. (17 pages)
  • Thomas D. Schneider, "Information and Entropy of Patterns in Genetic Switchs," Maximum-Entropy and Bayesian Methods in Science and Engineering, vol. 2, pp. 147-154, 1988.
  • Otto G. Berg, et al., "Selection of DNA Binding Sites by Regulatory Proteins: Statistical-Mechanical Theory and Application to Operators and Promoters," Journal of Molecular Biology, vol. 193, No. 4, pp. 723-750, Feb. 20, 1987. (21 pages)
  • Rodger Staden, "Computer Methods to Locate Signals in Nucleic Acid Sequences," Nucleic Acids Research, vol. 12, No. 1, pp. 505-519, 1984. (15 pages)
  • Gary D. Stormo, et al., "Use of the `Perceptron` Algorithm to Distinguish Translational Initiation Sites in E. coli," Nucleic Acids Research, vol. 10., No. 9, pp. 2997-3011, 1982. (15 pages)


  • Inquire Regarding Licensing

    Powered by Verity


    Plaques from Patent Awards      Gallery of Obscure PatentsNominate this for the Gallery...

    Thomson Reuters Copyright © 1997-2010 Thomson Reuters 
    Subscriptions  |  Web Seminars  |  Privacy  |  Terms & Conditions  |  Site Map  |  Contact Us  |  Help