|
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.
USAGE: stochastic <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 partition)
-
Sequence file (holds sequence: .seq or .fasta)
Note that in order to use a squence file, the "sequence"
flag must be specified (see "--sequence" below).
Also, note that nucleotides in lower-case will be forced single-stranded.
|
| <ct file> |
The name of a CT file to which output structures 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. |
| --sequence |
Identify the input file format as a sequence file. |
| -e, -E, --ensemble |
Specify the 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.
|
1. Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics, 11:129. (2010).
2. Harmanci, A.O., Sharma, G. and Mathews, D.H.
"Stochastic sampling of the RNA structural alignment space.
Nucleic Acids Res., 37, 4063-4075.
(2009)
3. Ding, Y. and Lawrence, C.E.
"A statistical sampling algorithm for RNA secondary structure prediction."
Nucleic Acids Res., 31, 7280-7301.
(2003) | 