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Conserved RNA Secondary Structures in Picornaviridae Genomes

Author

Listed:
  • C. Witwer
  • S. Rauscher
  • I. L. Hofacker
  • P. F. Stadler

Abstract

The family Picornaviridae contains important pathogens including, for example, Hepatitis A virus and Foot-and-Mouth Disease Virus. The genome of these viruses is a single messenger-active (+)-RNA of 7200 to 8500nts. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, among them an IRES region toward the 5'end. This contribution provides a comprehensive computational survey of the complete genomic RNAs and a detailed comparative analysis of the conserved structural elements in seven of the currently nine genera in the family Picornaviridae. Compared with previous studies we find: (1) that only smaller sections of the IRES region than previously reported are conserved at single-base-pair resolution, and (2) that there is a number of significant structural elements in the coding region. Furthermore we identify potential CREs in four genera where this feature has not been reported so far.

Suggested Citation

  • 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.
    • Handle: RePEc:wop:safiwp:01-08-040
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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. 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.
    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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