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]
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).
||The name of a CT file to which output will be written.
|-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.
||Identify the input file format as a sequence file.
|-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.
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.
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).