Prediction of RNA base pairing probabilities
using massively parallel computers
Martin Fekete, Ivo L. Hofacker, and Peter F. Stadler
We present an implementation of McCaskill's
algorithm for computing the base pair probabilities of an RNA molecule
for massively parallel message passing architectures. The program can
be used to routinely fold RNA sequences of more than 10000
nucleotides. Applications to complete viral genomes are discussed.
RNA Secondary Structure Prediction, Message Passing, Parallel Computer
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