RNAduplex − manual page for RNAduplex 2.4.18
Compute the structure upon hybridization of two RNA strands
reads two RNA
sequences from stdin or <filename> and computes
optimal and suboptimal secondary structures for their
hybridization. The calculation is simplified by allowing
only inter−molecular base pairs, for the general case
use RNAcofold. The computed optimal and suboptimal structure
are written to stdout, one structure per line. Each line
consist of: The structure in dot bracket format with a
"&" separating the two strands. The range of
the structure in the two sequences in the format
"from,to : from,to"; the energy of duplex
structure in kcal/mol. The format is especially useful for
computing the hybrid structure between a small probe
sequence and a long target sequence.
Print help and exit
Print help, including all details and hidden options, and exit
Print help, including hidden options, and exit
Print version and exit
Below are command line options which alter the general behavior of this program
sort the printed output by free energy
Do not automatically substitude nucleotide "T" with "U"
Select additional algorithms which should be included in the calculations.
Compute suboptimal structures with energy in a certain range of the optimum (kcal/mol). Default is calculation of mfe structure only.
Rescale energy parameters to a temperature of temp C. Default is 37C.
Do not include special tabulated stabilizing energies for tri−, tetra− and hexaloop hairpins. Mostly for testing.
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.
Produce structures without lonely pairs (helices of length 1).
For partition function folding this only disallows pairs that can only occur isolated. Other pairs may still occasionally occur as helices of length 1.
Do not allow GU pairs
Do not allow GU pairs at the end of helices
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.
Allow other pairs in addition to the usual AU,GC,and GU pairs.
Its argument is a comma separated list of additionally allowed pairs. If the first character is a "−" then AB will imply that AB and BA are allowed pairs. e.g. RNAfold −nsp −GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy.
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
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
Ivo L Hofacker, Ronny Lorenz
If in doubt our program is right, nature is at fault. Comments should be sent to email@example.com.