| ## RNAstructure Command Line Help stochastic and stochastic-smp | ### Contents ### Index
stochastic is used to sample secondary structures from the Boltzman enemble. The probability of sampling a given structure is proportional to the probability that it occurs. stochastic-smp is a parallel processing version for use on multi-core computers, built using OpenMP. ### USAGE: stochastic <input file> <ct file> [options] ### OR: stochastic-smp <input file> <ct file> [options] ### Required parameters:
<input file> | The name of a file containing input data. This input data can be in one of two formats: Partition function save file (holds base pairing probability data for all pairs and can be generated using the partition interface). Sequence file (holds raw sequence: .seq or .fasta). Note that lowercase nucleotides are forced single-stranded in structure prediction. Note that in order to use a squence file, the "sequence" flag must be specified (see "--sequence" below).
<ct file> | The name of a CT file to which output will be written.
### Options that do not require added values:
-d, -D, --DNA | This flag only matters if the input file is a sequence file and has been identified as such (see "--sequence" below). 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.
--sequence | Identify the input file format as a sequence file.
### Options that require added values:
-e, -E, --ensemble | Specify the ensemble sample size. Default is 1000 structures.
-s, -S, --seed | Specify the random number seed as an integer. Using a different seed will result in a different sample of structures. Default is 1234.
### Notes for smp: stochastic-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: Reuter, J.S. and Mathews, D.H. "RNAstructure: software for RNA secondary structure prediction and analysis." BMC Bioinformatics, 11:129. (2010). Harmanci, A.O., Sharma, G. and Mathews, D.H. "Stochastic sampling of the RNA structural alignment space." Nucleic Acids Res., 37:4063-4075. (2009). Ding, Y. and Lawrence, C.E. "A statistical sampling algorithm for RNA secondary structure prediction." Nucleic Acids Res., 31:7280-7301. (2003).