Individual Information Theory and Sequence Walkers

Individual information theory and sequence walkers can be used to completely replace consensus sequences in molecular biology. The methods are consistent with other applications of information theory to the study of binding sites and they do not use arbitrary "scores". This technology is available for license. For more information please contact us!

• Movie of a walker
  

• Glossary definition of sequence walkers

• Delila Server for sequence walkers

• About the relationship between Logos and Walkers

  

• The example given here shows the effect of a mutation that causes blindness, found by R. Allikmets and M. Dean.
  

• A poster on walkers and individual information was shown at NIH in December 1995.

• Sequence walkers and RNA folding

• Papers

  • The basic paper describing individual information theory is

    @article{Schneider.Ri,
    author = "T. D. Schneider",
    title = "Information Content of Individual Genetic Sequences",
    journal = "J. Theor. Biol.",
    volume = "189",
    number = "4",
    pages = "427-441",
    note = "http://www.ccrnp.ncifcrf.gov/$\sim$toms/paper/ri/",
    year = "1997"}
    

  • This paper describes walkers:

    @article{Schneider.walker,
    author = "T. D. Schneider",
    title = "Sequence Walkers:
    a graphical method to display how binding proteins
    interact with {DNA} or {RNA} sequences",
    comment = "walker.tex",
    journal = "Nucl. Acids Res.",
    volume = "25",
    note = "November 1, issue 21",
    pages = "4408-4415",
    year = "1997"}
    

  • A paper describing the use of individual information for understanding splice junctions for medical diagnosis is:

    @article{Rogan.Schneider.hmsh2.1995,
    author = "P. K. Rogan
     and T. D. Schneider",
    title = "Using Information Content and Base Frequencies
    to Distinguish Mutations from Genetic Polymorphisms in Splice Junction
    Recognition Sites",
    journal = "Human Mutation",
    volume = "6",
    pages = "74-76",
    year = "1995"}
    

  • A paper describing the use of individual information for understanding the Fis protein is:

    @article{Hengen.fisinfo,
    author = "P. N. Hengen
     and S. L. Bartram
     and L. E. Stewart
     and T. D. Schneider",
    title = "Information Analysis of {Fis} Binding Sites",
    comment = "fisinfo.tex",
    journal = "Nucl. Acids Res.",
    volume = "25",
    number = "24",
    pages = "4994-5002",
    year = "1997"}
    

  • A paper describing the use of individual information for medical diagnosis is:

    @article{Rogan.Faux.Schneider1998,
    author = "P. K. Rogan
     and B. M. Faux
     and T. D. Schneider",
    title = "Information analysis of human splice site mutations",
    journal = "Human Mutation",
    volume = "12",
    pages = "153-171",
    year = "1998"}
    

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• PATENT

  Because of its clinical applications, NIH and Penn State have obtained a patent on the individual information and walker technique: ``Computational analysis of nucleic acid information defines binding sites'' (US Ser. No. PCT/US96/11088) was allowed in July 1997.

  Patent 5867402 issued 1999 Feburary 2: Computational analysis of nucleic acid information defines binding sites Thomas D. Schneider and Peter K. Rogan
  

• This is a short formal non-confidential disclosure about the invention.

• Contacts for licensing Walker software

  If you are interested in using Scan, Walker and newer tools not shown here, please contact us for licensing or materials transfer agreements. Licensing applies to commercial use or commercial development, while materials transfer agreements apply to research and education. We encourage interested parties to sign a confidential disclosure agreement to obtain further details about these methods and to obtain the programs. The purpose of these agreements is to protect the patent for commercial applications, not to restrict the use of the methods by educators and researchers.

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• What is in the individual information program package?

• What computer resources do I need to use the individual information program package? Be sure to check this before setting up the agreement!

• How to Prepare Yourself for Using Walkers

Schneider Lab
origin: 1996 Feb 27
updated: 2008 Jeb 1