RNAdos − manual page for RNAdos 2.4.18
Calculate the density of states for each energy band of an RNA
reads an RNA sequence and computes the density of states for
each energy band.
Print help and exit
Print help, including all details and hidden options, and exit
Print version and exit
Command line options which alter the general behavior of this program
The RNA sequence (ACGU)
Structures are only counted until this threshold is reached. Default is 0 kcal/mol.
Set the number of threads used for calculations (only available when compiled with OpenMP support)
Rescale energy parameters to a temperature of temp C. Default is 37C.
How to treat "dangling end" energies for bases adjacent to helices in free ends and multi−loops
With −d1 only unpaired bases can participate in at most one dangling end. With −d2 this check is ignored, dangling energies will be added for the bases adjacent to a helix on both sides in any case; this is the default for mfe and partition function folding (−p). The option −d0 ignores dangling ends altogether (mostly for debugging). With −d3 mfe folding will allow coaxial stacking of adjacent helices in multi−loops. At the moment the implementation will not allow coaxial stacking of the two interior pairs in a loop of degree 3 and works only for mfe folding.
Note that with −d1 and −d3 only the MFE computations will be using this setting while partition function uses −d2 setting, i.e. dangling ends will be treated differently.
Read energy parameters from paramfile, instead of using the default parameter set.
Different sets of energy parameters for RNA and DNA should accompany your distribution. See the RNAlib documentation for details on the file format. When passing the placeholder file name "DNA", DNA parameters are loaded without the need to actually specify any input file.
Set the size of the hash table for each cell in the dp−matrices.
If you use this program in your work you might want to cite:
R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011), "ViennaRNA Package 2.0", Algorithms for Molecular Biology: 6:26
I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994), "Fast Folding and Comparison of RNA Secondary Structures", Monatshefte f. Chemie: 125, pp 167-188
R. Lorenz, I.L. Hofacker, P.F. Stadler (2016), "RNA folding with hard and soft constraints", Algorithms for Molecular Biology 11:1 pp 1-13
J. Cupal, I.L. Hofacker, P.F. Stadler (1996), "Dynamic programming algorithm for the density of states of RNA secondary structures" Computer Science and Biology 96, Proc. German Conf. on Bioinformatics 1996, pp. 184-186.
The energy parameters are taken from:
D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M. Zuker, D.H. Turner (2004), "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure", Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292
D.H Turner, D.H. Mathews (2009), "NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure", Nucleic Acids Research: 38, pp 280-282
Gregor Entzian, Ronny Lorenz
If in doubt our program is right, nature is at fault. Comments should be sent to firstname.lastname@example.org.