CUDA RNAfold-Reference-Cited by-同舟云学术

CUDA RNAfold

Published:2018-04-11 Issue: Volume: Page:
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Author:

Langdon W. B.,Lorenz Ronny

Abstract

AbstractWe add CUDA GPU C program code to RNAfold to enable both it to be run on nVidia gaming graphics hardware and so that many thousands of RNA secondary structures can be computed in parallel. RNAfold predicts the folding pattern for RNA molecules by using O(n3) dynamic programming matrices to minimise the free energy of treating them as a sequence of bases. We benchmark RNAfold on RNA STRAND and artificial sequences of upto 30 000 bases on two GPUs and a GPGPU Tesla. The speed up is variable but up to 14 times.

Publisher

Cold Spring Harbor Laboratory

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