RNAALIDUPLEX(1)

Okay bestie, this is RNAALIDUPLEX(1) 🎀, the User Commands page for RNAaliduplex. It's giving everything you need 💅

✨ NAME ✨

RNAaliduplex — manual page for RNAaliduplex 2.7.0 💖

💅 SYNOPSIS 💅

RNAaliduplex [options] <file1.aln> <file2.aln>

🦋 DESCRIPTION 🦋

RNAaliduplex 2.7.0 🌸

Predict conserved RNA-RNA interactions between two alignments 🔥

Okay so this program reads two alignments of RNA sequences in CLUSTAL format and predicts optimal and suboptimal binding sites, hybridization energies, and the structures that go with them ✨ It only counts inter-molecular base pairs, so if you need the general case, use RNAcofold. Using alignments lets you zoom in on binding sites that are evolutionarily conserved, which is so main character energy 👑 Just note that the two input alignments need the same number of sequences in the same order. So the 1st sequence in file1 gets hybridized to the 1st one in file2, and so on 🫶

The results (binding sites, energies, and structures) get printed to stdout, one structure per line 🧚 Each line has the structure in dot bracket format with a & separating the two strands, then the range in the two sequences formatted as from,to : from,to, then the energy of the duplex structure in kcal/mol. This is especially iconic for computing the hybrid structure between a small probe sequence and a long target sequence 🍓

• -h, --help — Prints help and exits 💅
• --detailed-help — Prints help including all the details and hidden options, then exits 🙈
• --full-help — Prints help including hidden options, then exits 🌈
• -V, --version — Prints the version and exits ⭐
• -v, --verbose — Be verbose (default=off) 🦋 This lowers the log level so even INFO messages get passed through.

🌈 Algorithms 🌈

Pick extra algorithms to include in the calculations 💜

• -e, --deltaEnergy=range — Computes suboptimal structures with energies within a certain range of the optimum (kcal/mol) ✨ By default you only get the mfe structure.
• -s, --sorted — Sorts the output by free energy 🫶 (default=off)

🌸 Energy Parameters 🌸

You can adapt energy parameter sets or load them from your own input files 🎀

• -T, --temp=DOUBLE — Rescales the energy parameters to a temperature of temp C 🔥 The default is 37C (default=37.0).
• -P, --paramFile=paramfile — Reads energy parameters from paramfile instead of the default parameter set 💖 Different sets of energy parameters for RNA and DNA should come with your distribution. Check the RNAlib documentation for the file format details. You can also use the placeholder file name DNA to load DNA parameters without actually specifying an input file 🧚
• -4, --noTetra — Skips the special tabulated stabilizing energies for tri-, tetra-, and hexaloop hairpins (default=off) 🙈 This one is mostly for testing, bestie.
• --salt=DOUBLE — Sets the salt concentration in molar (M). The default is 1.021M 🌊
• --saltInit=DOUBLE — Provides a salt correction for duplex initialization (in kcal/mol) 💅

🍓 Model Details 🍓

Tweak the energy model and pairing rules with these parameters 👑

• -d, --dangles=INT — Decides how to treat "dangling end" energies for bases next to helices in free ends and multi-loops (default=2) 🦋 With -d1, only unpaired bases can take part in at most one dangling end. With -d2, that check gets skipped, and dangling energies are added for bases next to a helix on both sides no matter what. This is the default for mfe and partition function folding (-p). -d0 ignores dangling ends altogether (mostly for debugging). -d3 lets mfe folding allow coaxial stacking of adjacent helices in multi-loops. Right now, the implementation won't 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. Partition function uses the -d2 setting, so dangling ends get treated differently 😭

• --noLP — Produces 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 — Doesn't allow GU pairs (default=off) 🙅‍♀️
• --noClosingGU — Doesn't allow GU pairs at the end of helices (default=off) 💜
• --nsp=STRING — Allows other pairs on top of the usual AU, GC, and GU pairs 🌈 The argument is a comma separated list of extra allowed pairs. If the first character is a -, then AB will imply that AB and BA are both allowed. For example, --nsp="-GA" allows GA and AG pairs. Nonstandard pairs get 0 stacking energy 🧚
• --helical-rise=FLOAT — Sets the helical rise of the helix in Angstrom units (default=2.8) ⚠️ Use with caution! This value gets reset automatically to 3.4 if DNA parameters are loaded via -P DNA and no further value is provided.
• --backbone-length=FLOAT — Sets the average backbone length for looped regions in Angstrom units (default=6.0) ⚠️ Use with caution! This value gets reset automatically to 6.76 if DNA parameters are loaded via -P DNA and no further value is provided.
• --log-level=level — Sets the 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 informational messages. Log-level 5 turns off all messages, even errors and other critical info 🙈
• --log-file[=filename] — Prints log messages to a file instead of stderr (default=RNAaliduplex.log) 🎀
• --log-time — Includes a time stamp in log messages (default=off) ⏰
• --log-call — Includes the file and line of the log calling function (default=off) 🔍

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📚 REFERENCES 📚

If you use this program in your work, you might want to cite these bestie 🫶

• 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 come from these papers 🧚

• 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 🦋

RNAduplex(1) RNAcofold(1) RNAfold(1) ✨

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Bestie, that's the whole page 💖 RNAaliduplex 2.7.0, February 2026, all yours now 🎀✨