RNAaliduplex − manual page for RNAaliduplex 2.4.11
RNAaliduplex [options] <file1.aln> <file2.aln>
Predict conserved RNA−RNA interactions between two alignments
The program reads two alignments of RNA sequences in CLUSTAL format and predicts optimal and suboptimal binding sites, hybridization energies and the corresponding structures. The calculation takes only inter−molecular base pairs into account, for the general case use RNAcofold. The use of alignments allows one to focus on binding sites that are evolutionary conserved. Note, that the two input alignments need to have equal number of sequences and the same order, i.e. the 1st sequence in file1 will be hybridized to the 1st in file2 etc.
binding sites, energies, and structures 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
Print help and exit
Print help, including all details and hidden options, and exit
Print version and exit
Below are command line options which alter the general behavior of this program
Compute suboptimal structures with energy in a certain range of the optimum (kcal/mol). Default is calculation of mfe structure only.
print output sorted by free energy
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
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.
Read energy parameters from paramfile, instead of using the default parameter set.
A sample parameter file should accompany your distribution. See the RNAlib documentation for details on the file format.
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 firstname.lastname@example.org.