CUDA-Sankoff is a tool that performs the optimal RNA structural alignment. We developed a CPU version (bin/sankoff) and a GPU version (bin/cuda_sankoff).
This software have been developed and tested on Linux, and it should work on all major distributions.
You need a modern C++ compiler. In Ubuntu, you can install it by:
sudo apt-get install build-essential libboost-dev
You also need the CUDA SDK. Check how to install it on the NVIDIA page:
https://developer.nvidia.com/cuda-downloads
You also, need to Download Vienna RNA library, compile it in the folder 'ViennaRNA-2.3.3'. Check the instructions inside this folder.
To compile, you enter the "cuda_sankoff" folder and type:
'make'
This works in all major Linux distributions and the 'bin/sankoff' and 'bin/cuda_sankoff' binaries will be available.
Few examples:
#Easy test:
./bin/sankoff seqs/025.fasta
#Easy test:
./bin/cuda\_sankoff seqs/050.fasta
Check the 'cuda_sankoff/seqs/' folder for other tests.
Usually the default options are the best to run. You can change and check more at:
./bin/sankoff -h
D. Sundfeld, G. Teodoro, J. H. Havgaard, J. Gorodkin, and A. C. M. A. Melo. Using GPU to accelerate the pairwise structural RNA alignment with base pair probabilities. Concurrency and computation practice and experience, Accepted, 2019.
D. Sundfeld, J. H. Havgaard, J. Gorodkin, and A. C. M. A. Melo. CUDA-Sankoff: Using GPU to accelerate the pairwise structural RNA alignment. In 25th Euromicro International Conference on Parallel, Distributed and Network-based Processing, PDP 2017, 2017, pages 295–302, 2017.
This project is licensed under the MIT License