Rsample is used to calculate the
partition function for a sequence that has multiple conformations.
To perform a complete Rsample calculation, the following steps
should be performed:
- Run Rsample, using the options listed below, to produce a Partition Save File (PFS)
- Run
stochastic, using this PFS file as input, to produce a CT
file with Boltzmann ensemble of 1,000 structures.
- Read the CT file from step 2 (as a command line argument in
Linux and MacOS) with R script RsampleCluster.R (optionally depends on calcdistf90.R and calcdist.f90).
This program uses the algorithm by Ding and Lawrence to
calculate optimal number of clusters and their
centroids. In addition to R, it requires the installation of R package with clustering procedures called fpc which can be
done by typing install.packages("fpc") inside R.
Rsample-smp is a parallel processing version for use on multi-core
computers, built using OpenMP.
USAGE: Rsample <seq file> <restraints
file> <pfs file> [options]
OR: Rsample-smp <seq file>
<restraints file> <pfs file> [options]
| <seq file> |
The name of a sequence
file containing input data.
Note that lowercase nucleotides are forced single-stranded
in structure prediction. |
| <restraints file> |
Specify a file with experimental restraints. SHAPE
data file format should be used. |
| <pfs file> |
The name of a binary partition function save file to
which output will be written. |
| -d, -D, --DNA |
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. |
| -v, -V, --version |
Display version and copyright information for this
interface. |
| -c, --cparam |
Specify a C parameter used in Rsample calculations.
Default value derived for SHAPE experiments is 0.5
kcal/mol. |
| -O, --offset |
Specify and offset parameter used in Rsample
calculations.
Default value derived for SHAPE experiments is 1.1
kcal/mol. |
| -ns, --numsamples |
Specify number of samples for stochastic sampling
calculation used in Rsample.
Default is 10,000. |
| -s, --seed |
Specify a random seed.
Default is to set random seed from current time. |
| -rPE, --reactPairedEnd |
Give full path to file with end-of-helix paired
nucleotide reactvities dataset.
Default values (from SHAPE experiments) are in rsample
directory in DATAPATH. |
| -rPM, --reactPairedMiddle |
Give full path to file with middle-of-helix paired
nucleotide reactvities dataset.
Default values (from SHAPE experiments) are in rsample
directory in DATAPATH. |
| -rUP, --reactUnpaired |
Give full path to file with unpaired nucleotide
reactvities dataset.
Default values (from SHAPE experiments) are in rsample
directory in DATAPATH. |
| -t, -T, --temperature |
Specify the temperature at which calculation takes
place in Kelvin.
Default is 310.15 K, which is 37 degrees C. |
| -md, --maxdistance |
Specify a maximum paired distance between nucleotides.
Default is no restriction on distance between pairs.
|
Rsample-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).
- Spasic, A., Assmann, S.M., Bevilacqua,
P.C. and Mathews, D.H.
"Modeling RNA secondary structure folding ensemble using SHAPE
mapping data."
Manuscript in preparation.
- Ding, Y. and Lawrence, C.E.
"A statistical sampling algorithm for RNA secondary structure
prediction."
Nucleic Acids Research, 31:7280 (2003).
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