EDcalculator is used to calculate the Ensemble Defect (ED) of a
structure or structures in a CT
file or Dot-Bracket
file. This is the average number of nucleotides (as estimated by a partition function calculation) that will not be paired as expected in the structure, for the specific sequence and structure in the input ct or dot-bracket file.
EDcalculator-smp is a parallel processing version for use on
The program outputs both the total ED and the normalized ED
(NED; i.e. the total divided by the number of nucleotides in the
sequence). The program can also calculate the ED for a local region of the structure. The region is specified using --start and --end (inclusive), and the normalized ED is the ED divided by the fragment length. The default behavior is to use the full length of the sequence.
USAGE: EDcalculator <structure file> [options]
OR: EDcalculator-smp <structure file> [options]
||The name of a CT file
file containing the input structure. The ED is calculated for this sequence to fold to the structure encoded in the input file.
|-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.
|| Output just the *Normalized* ensemble defect as a pure
number (with no
|-v -V --version
||Display version and copyright information for this
|-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.
||Output the results to the specified file instead of to
the screen (stdout).
||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.
|-s -S --start
||Specify a start nucleotide for a local calculation. The default is to start at the first nucleotide (nucleotide 1).
|-e -E --end
||Specify an end nucleotide for a local calculation. The default is to end at the last nucleotide of the sequence.
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
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).