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Automatic Detection of of Conserved Base Pairing Patterns in RNA Virus Genomes

Author

Listed:
  • Ivo L. Hofacker
  • Peter F. Stadler

Abstract

Almost all RNA molecules - and consequently also almost all subsequences of a large RNA molecule - form secondary structures. The presence of secondary structure in itself therefore does not indicate any functional significance. In fact, we may not expect a conserved secondary structure for all parts of a viral genome or a mRNA, even if there is a significant level of sequence conservation.

Suggested Citation

  • Ivo L. Hofacker & Peter F. Stadler, 1998. "Automatic Detection of of Conserved Base Pairing Patterns in RNA Virus Genomes," Working Papers 98-06-058, Santa Fe Institute.
    • Handle: RePEc:wop:safiwp:98-06-058
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    References listed on IDEAS

    as
    1. Ivo L. Hofacker & Martin Fekete & Christoph Flamm & Martijn A. Huynen & Susanne Rauscher & Paul E. Stolorz & Peter F. Stadler, 1998. "Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes," Working Papers 98-02-020, Santa Fe Institute.
    2. Stefan Wuchty & Walter Fontana & Ivo L. Hofacker & Peter Schuster, 1998. "Complete Suboptimal Folding of RNA and the Stability of Secondary Structures," Working Papers 98-05-040, Santa Fe Institute.
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    Cited by:

    1. Andreas Wagner & Peter F. Stadler, 1999. "Viral RNA and Evolved Mutational Robustness," Working Papers 99-02-010, Santa Fe Institute.

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    1. C. Witwer & S. Rauscher & I. L. Hofacker & P. F. Stadler, 2001. "Conserved RNA Secondary Structures in Picornaviridae Genomes," Working Papers 01-08-040, Santa Fe Institute.
    2. Martin Fekete & Ivo L. Hofacker & Peter F. Stadler, 1998. "Prediction of RNA Base Pairing Probabilities Using Massively Parallel Computers," Working Papers 98-06-057, Santa Fe Institute.

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