CUDA RNAfold
Abstract
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.
02 /Specification & Classification
Click any tag to browse matching papers- Citations
- 1
- Research Focus
- Approach
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Enhancing RNA 3D Folding Prediction via Transformer and Equivariant Architectures under Resource Constraints
Ryan Mehra, Anshoo Mehra·bioRxiv·Jun 19, 2025
- Evolving better RNAfold C source code
William B. Langdon·bioRxiv·Oct 11, 2017
- RNA folding using quantum computers
Dillion M. Fox, Christopher M. MacDermaid, … Ross C. Walker·PLoS Computational BiologyPeer-reviewed·Apr 11, 2022
- De Novo RNA Tertiary Structure Prediction at Atomic Resolution Using Geometric Potentials from Deep Learning
Robin Pearce, Gilbert S. Omenn, Yang Zhang·bioRxiv·May 15, 2022
- rpcFold: residual parallel convolutional neural network to decipher RNA folding from RNA sequence
Nandita Sharma, Pralay Mitra·bioRxiv·Aug 26, 2024
- UFold: Fast and Accurate RNA Secondary Structure Prediction with Deep Learning
Laiyi Fu, Yingxin Cao, … Xiaohui S. Xie·Nucleic Acids ResearchPeer-reviewed·Oct 20, 2021