IDEAS home Printed from https://ideas.repec.org/p/wop/safiwp/95-10-099.html
   My bibliography  Save this paper

Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration

Author

Listed:
  • Walter Gruner
  • Robert Giegerich
  • Dirk Strothmann
  • Christian Reidys
  • Jacqueline Weber
  • Ivo L. Hofacker
  • Peter F. Stadler
  • Peter Schuster

Abstract

Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of all GC and AU sequences with chain lengths up to 30. The technique of tried is used for economic data storage and fast retrieval of information. The computed structural data are evaluated through exhaustive enumeration and used as an exact reference for testing analytical results derived from mathematical models and sampling based of statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them the structure of neural networks (being sets of sequences folding into the same structure), percolation of sequence space by neural networks, and the principle of shape space covering. The data of exhaustive enumeration are compared to the analytical results of a random graph model that reveals the generic properties of sequence to structure mappings based on some base pairing logic. The differences between the numerical and the analytical results are interpreted in terms of specific biophysical properties of RNA molecules.

Suggested Citation

  • Walter Gruner & Robert Giegerich & Dirk Strothmann & Christian Reidys & Jacqueline Weber & Ivo L. Hofacker & Peter F. Stadler & Peter Schuster, 1995. "Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration," Working Papers 95-10-099, Santa Fe Institute.
    • Handle: RePEc:wop:safiwp:95-10-099
    as

    Download full text from publisher

    To our knowledge, this item is not available for download. To find whether it is available, there are three options:
    1. Check below whether another version of this item is available online.
    2. Check on the provider's web page whether it is in fact available.
    3. Perform a search for a similarly titled item that would be available.

    References listed on IDEAS

    as
    1. Christian Reidys & Peter F. Stadler & Peter Schuster, 1995. "Generic Properties of Combinatory Maps: Neutral Networks of RNA Secondary Structures," Working Papers 95-07-058, Santa Fe Institute.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Christian Reidys & Peter F. Stadler & Peter Schuster, 1995. "Generic Properties of Combinatory Maps: Neutral Networks of RNA Secondary Structures," Working Papers 95-07-058, Santa Fe Institute.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Subbiah Baskaran & Peter F. Stadler & Peter Schuster, 1995. "Approximate Scaling Properties of RNA Free Energy Landscapes," Working Papers 95-10-083, Santa Fe Institute.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:wop:safiwp:95-10-099. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Thomas Krichel (email available below). General contact details of provider: https://edirc.repec.org/data/epstfus.html .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.