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ETEcalculator is used to estimate the end-to-end distance of a sequence. By default, tt generates a stochastic sample for an input sequence and then uses polymer physics to estimate the end-to-end distance in nanometers. The program can alternatively read a set of structures in ct format for which to estimate the end-to-end distance. ETEcalculator-smp is the parallel version built using OpenMP.
USAGE: ETEcalculator <sequence file> [options]
OR
ETEcalculator-smp <sequence file> [options]
| <seq file> or <ct file> |
Default: The name of a sequence
file containing input data. Note that lowercase nucleotides are forced single-stranded
in structure prediction.
The default can be changed to the name of a ct file by means of the --ct parameter. |
| --ct |
Specify that the input file name is the name of a ct file that contains structures. The default is to expect the name of a sequence. |
| -h, -H, --help |
Display the usage details message. |
| -r, --raw |
Output just the mean end-to-end distamce in nanometers. The default is to make output that is more verbose. |
| -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 |
Specify a filename to which the results will be written. The default is to write the output to STDOUT. |
| -n, --number |
Specify the size of the stochastic sample. The default is to use 1000 structures. |
| -s, -S, --seed |
Specify the random number seed. The default seed is 1234. |
ETEcalculator-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.
- Lai, W.C., Kayedkhordeh, M., Cornell, E.V., Farah, E., Bellaousov, S., Rietmeijer, R., Mathews, D.H., and Ermolenko, D.N.
"mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances."
Nature Communications. 9: 4328.(2018).
- Aalberts, D.P.and Nandagopa, N.
"A two length scale polymer theory for RNA loop free energies and helix stacking."
RNA, 16: 1350–1355 (2010).
- Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics, 11:129. (2010).
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