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Prediction of RNA Base Pairing Probabilities Using Massively Parallel Computers

Author

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

Abstract

We present an implementation of McCaskill's algorithm for computing the base pair probabilities of an RNA molecule for massively parallel message passing architectures. The program can be used to routinely fold RNA sequences of more than 10000 nucleotides. Applications to complete viral genomes are discussed.

Suggested Citation

  • 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.
    • Handle: RePEc:wop:safiwp:98-06-057
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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.
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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. 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.

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