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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. |
| <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. |
| -d |
Specify that the sequence is DNA, and DNA parameters are to be used.
Default is to use RNA parameters.
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| -h |
Display the usage details message. |
| -v |
Print the dynamic programming arrays to standard out, for debugging purposes. |
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Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction and analysis."
BMC Bioinformatics, 11:129. (2010).
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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).
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