Diana_Cluster.R clusters structures using DIANA clustering and reports the number of clusters and the centroids of the clusters. This follows the method of Ding et al. (2005). This is an R script available in scripts/.

USAGE: Rscript Diana_Cluster.R <ct file>

example: Rscript /home/username/RNAstructure/scripts/Diana_Cluster.R stochastic_sample.ct

Required parameters:

Notes:

Output is to standard out and a set of ct files. The program provides the number of clusters and their size. It also writes ct files with the centroids of each cluster in the format input_name.centroid.#.ct where input_name was the input filename and # is the number of the clsuter.

Required Packages:Diana_Cluster.R requires installation of the fpc package.

Set up RNAstructure: Diana_Cluster.R calls components of the RNAstructure package. Make sure to add the RNAstructure executables to your global path. The following steps show how to do so in Linux:
1- Use a command line-based text editor like nano to open up the bash profile in the users home directory. For example, use "nano ~/.bashrc"
2- Add this line to the file: export PATH=/path/to/RNAstructure/exe/:${PATH}
3- Add this line to the file: export DATAPATH=/path/to/RNAstructure/data_tables
4- Save changes and source the changed bashrc profile. You can use: source ~/.bashrc
On Apple OS, the steps are the same, but edit the file ~/.zshrc .
See Thermodynamics.html .

References:

1. Ding, Y., Chan, C.Y., and Lawrence, C.E.
   "RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble."
   RNA. 11: 1157-1166. (2005).
2. Reuter, J.S. and Mathews, D.H.
   "RNAstructure: software for RNA secondary structure prediction and analysis."
   BMC Bioinformatics, 11:129. (2010).
3. Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M. and Turner, D.H.
   "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure."
   Proc. Natl. Acad. Sci. USA, 101:7287-7292. (2004).