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RNAINVERSE(1) User Commands RNAINVERSE(1) NAME RNAinverse - manual page for RNAinverse 2.7.2 SYNOPSIS RNAinverse [OPTION]... DESCRIPTION RNAinverse 2.7.2 Find RNA sequences with given secondary structure The program searches for sequences folding into a predefined structure, thereby inverting the folding algorithm. Target structures (in bracket no- tation) 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 ap- pended. The -Fp and -R options can modify the output format, see command- line 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 is encountered. -h, --help Print help and exit --detailed-help Print help, including all details and hidden options, and exit --full-help Print help, including hidden options, and exit -V, --version Print version and exit -v, --verbose In conjunction with a negative value supplied to -R, print the last subsequence and substructure for each unsuccessful search. (default=off) Lower the log level setting such that even INFO messages are passed through. --log-level=level Set log level threshold. (default=`2') By default, any log messages are filtered such that only warnings (level 2) or errors (level 3) are printed. This setting allows for specifying the log level threshold, where higher values result in fewer information. Log-level 5 turns off all messages, even errors and other critical information. --log-file[=filename] Print log messages to a file instead of stderr. (default=`RNAin- verse.log') --log-time Include time stamp in log messages. (default=off) --log-call Include file and line of log calling function. (default=off) Algorithms: Select additional algorithms which should be included in the calcu- lations. -F, --function=mp Use minimum energy (-Fm), partition function folding (-Fp) or both (-Fmp). (default=`m') In partition function mode, the probability of the target structure exp(-E(S)/kT)/Q is maximized. This probability is written in brack- ets after the found sequence and Hamming distance. In most cases you'll want to use the -f option in conjunction with -Fp, see below. -f, --final=FLOAT In combination with -Fp stop search when sequence is found with E(s)-F is smaller than final, where F=-kT*ln(Q). -R, --repeat[=INT] Search repeatedly for the same structure. If an argument is sup- plied to this option it must follow the option flag immediately. E.g.: -R5 (default=`1') 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. -a, --alphabet=ALPHABET Find sequences using only nucleotides from a given alphabet. Energy Parameters: Energy parameter sets can be adapted or loaded from user-provided input files -T, --temp=DOUBLE Rescale energy parameters to a temperature of temp C. Default is 37C. (default=`37.0') -P, --paramFile=paramfile 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 para- meters are loaded without the need to actually specify any input file. -4, --noTetra Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. (default=off) Mostly for testing. --salt=DOUBLE Set salt concentration in molar (M). Default is 1.021M. Model Details: Tweak the energy model and pairing rules additionally using the fol- lowing parameters -d, --dangles=INT How to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops (default=`2') 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 debug- ging). 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 enclosed 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. dan- gling ends will be treated differently. --noGU Do not allow GU pairs. (default=off) --noClosingGU Do not allow GU pairs at the end of helices. (default=off) --nsp=STRING 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. --energyModel=INT Set energy model. Rarely used option to fold sequences from the artificial ABCD... al- phabet, where A pairs B, C-D etc. Use the energy parameters for GC (--energyModel 1) or AU (--energyModel 2) pairs. --helical-rise=FLOAT Set the helical rise of the helix in units of Angstrom. (default=`2.8') Use with caution! This value will be re-set automatically to 3.4 in case DNA parameters are loaded via -P DNA and no further value is provided. --backbone-length=FLOAT Set the average backbone length for looped regions in units of Angstrom. (default=`6.0') Use with caution! This value will be re-set automatically to 6.76 in case DNA parameters are loaded via -P DNA and no further value is provided. REFERENCES 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 se- quences 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. Su- san, M. Zuker, D.H. Turner (2004), "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA sec- ondary 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", Nu- cleic Acids Research: 38, pp 280-282 EXAMPLES To search 5 times for sequences forming a simple hairpin structure inter- rupted by one GA mismatch call $ RNAinverse -R 5 and enter the lines (((.(((....))).))) NNNgNNNNNNNNNNaNNN AUTHOR Ivo L Hofacker REPORTING BUGS If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at. RNAinverse 2.7.2 December 2025 RNAINVERSE(1)
NAME | SYNOPSIS | DESCRIPTION | REFERENCES | EXAMPLES | AUTHOR | REPORTING BUGS
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