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.

Keywords: RNA Secondary Structure Prediction, Message Passing, Parallel Computer

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