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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]
| <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).
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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).
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| <ct file> |
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.
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| -h, -H, --help |
Display the usage details message. |
| --sequence |
Identify the input file format as a sequence file. |
| -e, -E, --ensemble |
Specify the ensemble sample size.
Default is 1000 structures.
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| -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.
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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.
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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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Harmanci, A.O., Sharma, G. and Mathews, D.H.
"Stochastic sampling of the RNA structural alignment space."
Nucleic Acids Res., 37:4063-4075. (2009).
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Ding, Y. and Lawrence, C.E.
"A statistical sampling algorithm for RNA secondary structure prediction."
Nucleic Acids Res., 31:7280-7301. (2003).
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