|
design attempts to
find a nucleic acid sequence that will fold to a given
structure.
USAGE: design <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. |
| -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. |
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