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Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes

Author

Listed:
  • Ivo L. Hofacker
  • Martin Fekete
  • Christoph Flamm
  • Martijn A. Huynen
  • Susanne Rauscher
  • Paul E. Stolorz
  • Peter F. Stadler

Abstract

We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and phylogenetic comparison. In contrast to purely phylogenetic methods, our algorithm can be used for small data sets of about 10 sequences, efficiently exploiting the information contained in the sequence variability. The procedure constructs a prediction only for those parts of sequences that are consistent with a single conserved structure. Our implementation produces reasonable consensus structures without user interference. As an example we have analyzed complete HIV-1 and Hepatitis C virus genomes as well as the small segment of Hanta virus. Our method confirms the known structures in HIV-I and predicts previously unknown conserved RNA secondary structures in HCV.

Suggested Citation

  • 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.
    • Handle: RePEc:wop:safiwp:98-02-020
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    Cited by:

    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.
    3. 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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