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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