| ## RNAstructure Command Line Help ETEcalculator | ### Contents ### Index
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] ### Required parameters:
<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.
### Options that do not require added values:
--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.
### Options that require added values:
-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.
### Notes for smp: 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. ### References: 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).