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RNAstructure Command Line Help

design attempts to find a nucleic acid sequence that will fold to a given structure. 

USAGE: design <input file>  [-o <output file>]  [options]

Required parameters:

<input file> A structure (CT or Dot-Bracket) file that indictates the target structure. (The sequence in the file will be ignored.)

Options that do not require added values:

-d --dna Specify that the sequence is DNA, and DNA parameters are to be used. (The default is to use RNA parameters.)
-p --preselect
Specify that use pre-selected sequence segments should be used. (The default is that all nucleotides are chosen at random.)
-t --timer
Use a timer to measure the duration of the design process and print the elapsed time to standard output.
-h --help Display the usage details message.
-v --version
Display version and copyright information for this interface.

Options that require added values:

-a, -A, --alphabet Specify the name of a folding alphabet and associated nearest neighbor parameters. The alphabet is the prefix for the thermodynamic parameter files, e.g. "rna" for RNA parameters or "dna" for DNA parameters or a custom extended/modified alphabet. The thermodynamic parameters need to reside in the at the location indicated by environment variable DATAPATH.
The default is "rna" (i.e. use RNA parameters). This option overrides the --DNA flag.
-o --output Specify the output file. By default the resulting designed sequence is written to standard output only. This flag instructs the program to output the structure (in ct format) to the specified file.
-e --error
The maximum allowed ensemble defect per nucleotide.
-s --seed
Specify a random seed. The default is to use a seed based on the current system time. (It is necessary to specify a seed in order to get exactly reproducible results.)
-md --maxdepth Max-depth: The maximum extent to which the structure will be sub-divided in the binary decomposition. The default is 5.
-ml --maxleaf The maximum number of times a leaf can be re-optimized at random. The default is 3.
-mm --maxmutate The maximum number of times a nucleotide will be mutated during defect-weighted reoptimization. The default is 4.
-mr --maxredesign The maximum number of redesigns per parent node. The default is 10.