RNADUPLEX(1)

🎀 RNADUPLEX(1) — hi, it's RNAduplex 2.7.0 💖

Okay bestie, this is the manual page for RNAduplex, and I am OBSESSED with how it works ✨ It's the tool that figures out how two RNA strands cuddle up together 🧚

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✨ NAME ✨

RNAduplex — manual page for RNAduplex 2.7.0 🌸

💅 SYNOPSIS 💅

RNAduplex [OPTION]...

🦋 DESCRIPTION 🦋

RNAduplex 2.7.0 💜

Compute the structure upon hybridization of two RNA strands 🫶

Okay so this program reads two RNA sequences from stdin or <filename> and works out the best and next-best secondary structures for when they hybridize 😭 The calculation is simplified by only allowing inter-molecular base pairs (pairs between the two strands, not within one). If you need the general case, go use RNAcofold instead, it's giving full coverage 💀

The structures get written to stdout, one per line 🍓 Each line has three things: 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, and the energy of the duplex structure in kcal/mol. ngl this format is especially iconic for computing the hybrid structure between a small probe sequence and a long target sequence 🔥

• -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 — Be verbose. (default=off) ✨

Lowers the log level setting so even INFO messages get passed through 👀

🎀 I/O Options 🎀

Command line options for input and output (pre-)processing 💅

• -s, --sorted — Sort the printed output by free energy. (default=off) 🦋
• --noconv — Do not automatically substitute nucleotide T with U. (default=off) 🌸
• --log-level=level — Set log level threshold. (default=2) 🫶

By default, log messages are filtered so 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=RNAduplex.log) 📝
• --log-time — Include a time stamp in log messages. (default=off) ⏰
• --log-call — Include file and line of the log calling function. (default=off) 🔍

🌈 Algorithms 🌈

Select additional algorithms that should be included in the calculations 🧚

• -e, --deltaEnergy=range — Compute suboptimal structures with energy in a certain range of the optimum (kcal/mol). Default is calculation of the mfe structure only. 💜

⭐ 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, and you can check the RNAlib documentation for the file format details. The placeholder file name DNA can be used to load DNA parameters without actually specifying any input file, which is literally so convenient 🧬
• -4, --noTetra — Do not include the 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. 🌊
• --saltInit=DOUBLE — Provide salt correction for duplex initialization (in kcal/mol). 🧂

🦋 Model Details 🦋

Tweak the energy model and pairing rules with 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 allows 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 works only for mfe folding 🫠

Heads up bestie: with -d1 and -d3, only the MFE computations use this setting, while the partition function uses the -d2 setting, so dangling ends get treated differently 🚨

• --noLP — Produce structures without lonely pairs (helices of length 1). (default=off) 🌸

For partition function folding this only disallows pairs that can only occur isolated. Other pairs may still occasionally show up as helices of length 1 🥺

• --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. The argument is a comma separated list of additionally allowed pairs. If the first character is a -, then AB implies that AB and BA are allowed pairs, e.g. --nsp="-GA" will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy 🧩
• --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 🫣

📚 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 ✨

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 🧚

👑 AUTHOR 👑

Ivo L Hofacker, Ronny Lorenz 💖

🐛 REPORTING BUGS 🐛

If in doubt, our program is right and nature is at fault 🙃 Comments should be sent to rna@tbi.univie.ac.at 📬

🔗 SEE ALSO 🔗

RNAcofold(l), RNAfold(l) 💜

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Bye bestie, RNAduplex 2.7.0 from February 2026 is officially slaying 👑🦋🎀 🫶