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Generic Properties of Combinatory Maps: Neutral Networks of RNA Secondary Structures

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  • Christian Reidys
  • Peter F. Stadler
  • Peter Schuster

Abstract

Random graph theory is used to model relationships between sequences and secondary structure of RNA molecules. Sequences folding into identical structures form neutral networks which percolate sequence space if the fraction of neutral nearest neighbors exceeds a threshold value. The networks of any two different structures almost touch each other, and sequences folding into almost all "common" structures can be found in a small ball of an arbitrary location in sequence space. The results from random graph theory are compared with data obtained by folding large samples of RNA sequences. Differences are explained in terms of RNA molecular structures.

Suggested Citation

  • 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.
    • Handle: RePEc:wop:safiwp:95-07-058
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    1. 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.
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    Cited by:

    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.
    2. 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.

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