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