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RNAstructure Command Line Help

design attempts to find a nucleic acid sequence that will fold to a given structure. design-smp is the parallel processing version for multi-core calculations.

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

or design-smp <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.

Note that, by default, only A, C, G, U/T will be used in loops and A-U/T, G-C will be used in pairs. To use additional pairs or nucleotides, a bias file must be used.

-b --bias Specify a sequence bias for random selection of loop nucleotides and base pairs. The bias file format is defined here. Note that bias must be used with alphabets beyond A, C, G, U/T in order to use the additional nucleotides.
-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.


Note that pseudoknots cannot be designed with this program and that pseudoknots in the input structure are removed by the method of RemovePseudoknots (keeping the maximum number of pairs) at the start of the calculation.

Notes for smp:

design-smp, by default, will use all available compute cores for processing. The number of cores used can be controlled by setting the OMP_NUM_THREADS environment variable.



  1. Bellaousov, S., Kayedkhordeh, M., Peterson, R. J. & Mathews, D. H. (2018). Accelerated RNA Secondary Structure Design Using Pre-Selected Sequences for Helices and Loops. RNA. 24: 1555-1567.