| ## RNAstructure Command Line Help Fold-cuda | ### Contents ### Index
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] ### Required parameters:
<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.
<save file> | The name of a save file to which output will be written. This save file can be read by refold to predict structures.
### Options that do not require added values:
-d | Specify that the sequence is DNA, and DNA parameters are to be used. Default is to use RNA parameters.
-h | Display the usage details message.
-v | Print the dynamic programming arrays to standard out, for debugging purposes.
### ### References: 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).