Fold-cuda uses GPU acceleration to rapidly predict the lowest free energy structure and a set of suboptimal structures. This program implements only the time-consuming fill step of the calculation, and outputs a fold save file, like those generated by Fold -s. To generate structures, run the refold program on the output file.
Running this program requires CUDA and a CUDA-capable GPU.
USAGE: Fold-cuda <sequence or seq file> <save file> [options]
|<sequence or seq file>
A sequence can be given as a single string. If the entry is not a valid sequence (A,C,G,U,T only) then Fold-cuda will open a file.
A file needs to be a sequence file.
Note that lowercase nucleotides are not allowed in Fold-cuda, and lowercase nucleotides will generate an error message.
||The name of a save file to which output will be written. This save file can be read by refold to predict structures.
Specify that the sequence is DNA, and DNA parameters are to be used.
Default is to use RNA parameters.
||Display the usage details message.
||Print the dynamic programming arrays to standard out, for debugging purposes.
Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction and analysis."
BMC Bioinformatics, 11:129. (2010).
Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M. and Turner, D.H.
"Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure."
Proc. Natl. Acad. Sci. USA, 101:7287-7292. (2004).