TY - JOUR T1 - CUDA RNAfold JF - bioRxiv DO - 10.1101/298885 SP - 298885 AU - W. B. Langdon AU - Ronny Lorenz Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/04/11/298885.abstract N2 - We 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. ER -