RNA Folding on Parallel Computers: The Minimum Free Energy
Structures of Complete HIV Genomes
Ivo L. Hofacker, Martijn A. Huynen,
Peter F. Stadler, and Paul E. Stolorz
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.
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