RNAinverse − manual page for RNAinverse 2.4.11
Find RNA sequences with given secondary structure
searches for sequences folding into a predefined structure,
thereby inverting the folding algorithm. Target structures
(in bracket notation) and starting sequences for the search
are read alternately from stdin. Characters in the start
sequence other than "AUGC" (or the alphabet
specified with −a) will be treated as wild
cards and replaced by a random character. Any lower case
characters in the start sequence will be kept fixed during
the search. If necessary, the sequence will be elongated to
the length of the structure. Thus a string of "N"s
as well as a blank line specify a random start sequence. For
each search the best sequence found and its Hamming distance
to the start sequence are printed to stdout. If the the
search was unsuccessful, a structure distance to the target
is appended. The −Fp and −R
options can modify the output format, see commandline
options below. The program will continue to read new
structures and sequences until a line consisting of the
single character "@" or an end of file condition
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
Search repeatedly for the same structure. If an argument is supplied to this option it must follow the option flag immediately. E.g.: −R5
If repeats is negative search until −−repeats exact solutions are found, no output is done for unsuccessful searches. Be aware, that the program will not terminate if the target structure can not be found. If no value is supplied with this option, the default value is used.
Find sequences using only nucleotides from a given alphabet.
In conjunction with a negative value supplied to −R, print the last subsequence and substructure for each unsuccessful search.
Select additional algorithms which should be included in the calculations.
Use minimum energy (−Fm), partition function folding (−Fp) or both (−Fmp).
In partition function mode, the probability of the target structure exp(−E(S)/kT)/Q is maximized. This probability is written in brackets after the found sequence and Hamming distance. In most cases you’ll want to use the −f option in conjunction with −Fp, see below.
In combination with −Fp stop search when sequence is found with E(s)−F is smaller than final, where F=−kT*ln(Q).
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.
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.
A sample parameter file should accompany your distribution. See the RNAlib documentation for details on the file format.
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.
Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C−D etc. Use the energy parameters for GC (−e 1) or AU (−e 2) pairs.
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
D.H. Turner, N. Sugimoto, S.M. Freier (1988), "RNA structure prediction", Ann Rev Biophys Biophys Chem: 17, pp 167-192
M. Zuker, P. Stiegler (1981), "Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information", Nucl Acid Res: 9, pp 133-148
J.S. McCaskill (1990), "The equilibrium partition function and base pair binding probabilities for RNA secondary structures", Biopolymers: 29, pp 1105-1119
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
To search 5 times for sequences forming a simple hairpin structure interrupted by one GA mismatch call
$ RNAinverse -R 5
and enter the lines
Ivo L Hofacker
If in doubt our program is right, nature is at fault. Comments should be sent to email@example.com.