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RNA Folding on Parallel Computers: The Minimum Free Energy Structures of Complete HIV Genomes

Author

Listed:
  • Ivo L. Hofacker
  • Martijn A. Huynen
  • Peter F. Stadler
  • Paul E. Stolorz

Abstract

Secondary structure prediction is a standard tool in the analysis of RNA sequences. The prediction of RNA secondary structures is inherently non-local. This makes the analysis of long sequences (more than 4000 nucleotides) infeasible on present-day workstations. An implementation of the secondary structure prediction algorithm for hypercube-type parallel computers allows to compute efficientloy the structure of complete RNA virus genomes such as HIV-1 and other lentiviruses.

Suggested Citation

  • Ivo L. Hofacker & Martijn A. Huynen & Peter F. Stadler & Paul E. Stolorz, 1995. "RNA Folding on Parallel Computers: The Minimum Free Energy Structures of Complete HIV Genomes," Working Papers 95-10-089, Santa Fe Institute.
    • Handle: RePEc:wop:safiwp:95-10-089
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