RNAPDIST(1)

🦋 NAME 🦋

RNApdist - manual page for RNApdist 2.7.0 💖

💅 SYNOPSIS 💅

RNApdist [OPTION]...

✨ DESCRIPTION ✨

RNApdist 2.7.0 🌸

Okay bestie, this is the program that calculates distances between thermodynamic RNA secondary structures ensembles 🧬 It's giving science, and it's giving main character energy.

So here's the tea. It reads RNA sequences from stdin and then calculates structure distances between the thermodynamic ensembles of their secondary structures. Iconic. 👑

For each sequence, it computes the partition function and the matrix of base pairing probabilities. Then that probability matrix gets condensed into a vector that holds, for each base, the probabilities of being unpaired, paired upstream, or paired downstream. Lastly, those profiles get compared by a standard alignment algorithm. We are literally obsessed. 😭

It also saves the base pair probabilities as postscript "dot plots" (just like RNAfold 🍓) in files called name_dp.ps. The name is the name of the sequence, or a number if the sequence is unnamed. ✨

• -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) 📢 This lowers the log level setting so that even INFO messages get passed through.

🎀 I/O Options 🎀

Command line options for input and output (pre-)processing. Let's get this bread. 🍞

• --noconv — Do not automatically substitute nucleotide "T" with "U". (default=off) 🙅‍♀️
• --log-level=level — Set the log level threshold. (default=`2') 📝 By default, log messages are filtered so that only warnings (level 2) or errors (level 3) get printed. This setting lets you pick the threshold, and higher values mean fewer messages. 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=`RNApdist.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 that should be included in the calculations. Ooh, extra features. 🦋

• -X, --compare=p|m|f|c — Specify the comparison directive. (default=`p') 💜 Here are your options, babe:
  • -Xp compares the structures pairwise (p), so first with 2nd, third with 4th, and so on. 👯
  • -Xm calculates the distance matrix between all structures. The output is formatted as a lower triangle matrix. 🔺
  • -Xf compares each structure to the first one. 1️⃣
  • -Xc compares continuously, meaning the i-th with the (i+1)th structure. ➡️
• -B, --backtrack[=<filename>] — Print an "alignment" with gaps of the profiles. If <filename> is specified, the aligned structures get written there. (default=`none') 🧩 Within the profile output, these symbols are used:
  • () means essentially upstream (downstream) paired bases. 💖
  • {} means weakly upstream (downstream) paired bases. 🌙
  • | means strongly paired bases without preference. 💪
  • , means weakly paired bases without preference. 🍃
  • . means essentially unpaired bases. 🫧

If <filename> is not specified, the output goes to stdout, unless the "-Xm" option is set, in which case "backtrack.file" is used. 📄

🔮 Energy Parameters 🔮

Energy parameter sets can be adapted or loaded from user-provided input files. Customize your vibe. 🎨

• -T, --temp=DOUBLE — Rescale energy parameters to a temperature of temp C. The 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 come with your distribution. See the RNAlib documentation for details on the file format. If you pass the placeholder file name "DNA", DNA parameters get loaded without you needing to actually specify any input file. 🧬
• -4, --noTetra — Do not include the special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. (default=off) 🙈 This one is mostly for testing.
• --salt=DOUBLE — Set the salt concentration in molar (M). The default is 1.021M. 🧂

💜 Model Details 💜

Tweak the energy model and pairing rules with the following parameters. Let's get a little extra. 💅

• -d, --dangles=INT — Set the energy model for the treatment of dangling bases. (possible values="0", "2" default=`2') 🎭
• --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 occur 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 will imply that AB and BA are allowed pairs. For example, RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs get 0 stacking energy. 🌈
• --energyModel=INT — Set the energy model. This is a rarely used option for folding sequences from the artificial ABCD... alphabet, where A pairs B, C-D, and so on. 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 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 will be 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 these bops:

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 ✨

S. Bonhoeffer, J.S. McCaskill, P.F. Stadler, P. Schuster (1993), "RNA multi-structure landscapes", Euro Biophys J:22, pp 13-24 🌸

The energy parameters are taken from these two:

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 👑

Peter F Stadler, Ivo L Hofacker, Sebastian Bonhoeffer. The icons. 🫡

🙈 REPORTING BUGS 🙈

If in doubt our program is right, nature is at fault. 💀

Comments should be sent to rna@tbi.univie.ac.at. 📬

---

Bestie, that's the whole RNApdist 2.7.0 tea, February 2026 edition, filed under RNAPDIST(1). Go make some dot plots and slay the ensembles. 💅🦋🌈