RNAINVERSE(1)

✨ RNAINVERSE(1) 🦋 User Commands ✨

💖 NAME

bestie, okay so the whole name is RNAinverse, and this is the manual page for RNAinverse 2.7.0 🌸

🎀 SYNOPSIS

RNAinverse [OPTION]...

💅 DESCRIPTION

RNAinverse 2.7.0 💜

Find RNA sequences with given secondary structure 🧚

okay so this program basically does the folding algorithm backwards 🔥 it searches for sequences that fold into a structure you already picked. the target structures (in bracket notation) and the starting sequences get read alternately from stdin, so it's a whole back-and-forth vibe 🫶

a few lowkey important things 👀

• characters in the start sequence that aren't AUGC (or whatever alphabet you set with -a) become wild cards and get swapped for a random character 🎲
• any lower case characters in the start sequence stay fixed during the search 🔒
• if needed, the sequence gets elongated to the length of the structure 📏
• so a string of Ns, or a blank line, both mean "random start sequence" 🌈

for each search, the best sequence it finds and its Hamming distance to the start sequence get printed to stdout ✨ if the search was unsuccessful, a structure distance to the target gets tacked on at the end 💀 the -Fp and -R options can change the output format, so check the commandline options below 👇

the program keeps reading new structures and sequences until it hits a line with just the single character @, or an end of file condition 🏁

• -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)

it also lowers the log level setting so even INFO messages get through 📢

• --log-level=level — set the log level threshold. (default=2)

by default only warnings (level 2) or errors (level 3) get printed. higher values mean fewer messages, and log-level 5 turns off all messages, even errors and other critical stuff 🤫

• --log-file[=filename] — print log messages to a file instead of stderr. (default=RNAinverse.log) 📝
• --log-time — include a time stamp in log messages.

(default=off) ⏰

• --log-call — include the file and line of the log calling function.

(default=off) 🔍

🧚 Algorithms

select additional algorithms which should be included in the calculations 💜

• -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 gets 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 together with -Fp, see below 🫶

• -f, --final=FLOAT — in combination with -Fp, stop the search when a sequence is found with E(s)-F smaller than final, where F=-kT*ln(Q) 🛑
• -R, --repeat[=INT] — search repeatedly for the same structure. if an argument is supplied to this option it must follow the option flag immediately, e.g.: -R5 🔁

(default=1)

if repeats is negative, the search keeps going until --repeats exact solutions are found, and no output is done for unsuccessful searches. be warned: the program will not terminate if the target structure can't 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 you pass the placeholder file name DNA, DNA parameters get loaded without needing 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 even more using the following 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, and dangling energies get 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 enclosed pairs in a loop of degree 3, and it only works for mfe folding ⚠️

⚠️ heads up: with -d1 and -d3, only the MFE computations use this setting, while partition function uses the -d2 setting, so dangling ends get 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... alphabet, 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 gets re-set automatically to 3.4 if 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 gets re-set automatically to 6.76 if DNA parameters are loaded via -P DNA and no further value is provided ⚠️

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📚 REFERENCES

if you use this program in your work, you might want to cite these 🎓

• 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

🍓 EXAMPLES

to search 5 times for sequences forming a simple hairpin structure interrupted by one GA mismatch, call:

$ RNAinverse -R 5

and then enter the lines:

(((.(((....))).)))
NNNgNNNNNNNNNNaNNN

👑 AUTHOR

Ivo L Hofacker

🐛 REPORTING BUGS

if in doubt, our program is right and nature is at fault 🙃 comments should be sent to rna@tbi.univie.ac.at 💌

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🌈 ok that's the whole thing, bestie! RNAinverse 2.7.0 · February 2026 · RNAINVERSE(1) 🌈 💖