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EDcalculator is used to calculate the Ensemble Defect (ED) of a
structure or structures in a CT
file or Dot-Bracket
file. This is a measure of how much a single structure
deviates from the basepair probabilities calculated for the
ensemble of possible structures with the same sequence.
EDcalculator-smp is a parallel processing version for use on
multi-core computers.
The program outputs both the total ED and the"normalized" ED
(i.e. the total divided by the number of nucleotides in the
sequence).
USAGE: EDcalculator <structure file> [options]
OR: EDcalculator-smp <structure file> <energy
file> [options]
| -d, -D, --DNA |
Specify that the sequence is DNA, and DNA parameters
are to be used.
Default is to use RNA parameters. |
| -h, -H, --help |
Display the usage details message. |
| -r, --raw |
Output just the *Normalized* ensemble defect as a pure
number (with no
additional description). |
| -v -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. |
| -c -C --constraint |
Specify a folding constraints file to be applied. |
| -f --file |
Output the results to the specified file instead of to
the screen (stdout). |
| -n --number |
Specify the index of a particular structure for which
to calculate the defect. The default is -1, which means to
calculate the defect for all structures in the input file. |
The -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.
- Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics, 11:129. (2010).
- Bellaousov, S., Kayedkhordeh, M., Peterson, R. J. and Mathews, D. H.
"Accelerated RNA Secondary Structure Design Using Pre-Selected Sequences for Helices and Loops."
RNA. 24: 1555-1567. (2018).
- Zadeh, J.N., Wolfe, B.R., and Pierce, N.A.
"Nucleic acid sequence design via efficient ensemble defect optimization."
J. Comput. Chem., 32: 439-452. (2011).
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