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RNAstructure Command Line Help

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.



  1. Reuter, J.S. and Mathews, D.H.
    "RNAstructure: software for RNA secondary structure prediction and analysis."
    BMC Bioinformatics, 11:129. (2010).
  2. 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).