Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers

Abstract

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 10,000 nucleotides. Applications to complete viral genomes are discussed.

Keywords

RNA SECONDARY STRUCTURE RNA FOLDING RNA PARTITION FUNCTION PARALLEL COMPUTING MPI MESSAGE PASSING

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