RNA2DFOLD(1)

📦
version 2.7.0 · 5 versions
, in ubuntu resolute, ubuntu stonking

Okay bestie, welcome to the RNA2DFOLD(1) page 💖 (filed under User Commands, obviously 🎀)

✨ NAME ✨

RNA2Dfold - manual page for RNA2Dfold 2.7.0 🦋

✨ SYNOPSIS ✨

The whole vibe in one line 💅

RNA2Dfold [OPTION]...

✨ DESCRIPTION ✨

RNA2Dfold 2.7.0 🌸

Okay so this bad boy computes the MFE structure, the partition function, and representative sample structures of k,l neighborhoods 🔥

It slices the secondary structure space into (basepair)distance classes based on two fixed reference structures 🧚. You feed it a sequence plus two secondary structures in dot-bracket notation. Then, for each distance class, it works out the MFE representative, the Boltzmann probabilities, and the Gibbs free energy. ngl that's a lot of main character math 💜

On top of that, there's a stochastic backtracking routine that lets you pull samples of representative suboptimal secondary structures from each partition 🦋

  • -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 extra chatty 🗣️ (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 📥

  • -j, --numThreads=INT — set how many threads get used for calculations 🧵 (only available when compiled with OpenMP support)
  • --noconv — don't auto-swap nucleotide "T" for "U" 🙅 (default=off)
  • --log-level=level — set the log level threshold 📢 (default=`2')
    • By default, log messages get filtered so 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 info 😭
  • --log-file[=filename] — print log messages to a file instead of stderr 📝 (default=`RNA2Dfold.log')
  • --log-time — slap a time stamp on your log messages ⏰ (default=off)
  • --log-call — include the file and line of the log calling function 🔍 (default=off)

✨ Algorithms ✨

Pick any extra algorithms you want included in the calculations 🧮. The Minimum free energy (MFE) and a structure representative are calculated in any case, no cap.

  • -p, --partfunc — calculate the partition function, and thus the Boltzmann probabilities and Gibbs free energy 💅 (default=off)
  • --stochBT=INT — backtrack a certain number of Boltzmann samples from the appropriate k,l neighborhood(s) 🎲
  • --neighborhood=<k>:<l> — backtrack structures from a certain k,l-neighborhood only. You can specify this multiple times (<k>:<l>,<m>:<n>,...) 🎯
  • -K, --maxDist1=INT — the max distance to the first reference structure 📏
    • If this value is set, all structures that exhibit a basepair distance greater than maxDist1 get thrown into a distance class denoted K=L=-1 🗑️
  • -L, --maxDist2=INT — the max distance to the second reference structure 📏
    • If this value is set, all structures that exhibit a basepair distance greater than maxDist1 get thrown into a distance class denoted K=L=-1 🗑️ (the page literally says maxDist1 here too 🙈, so I'm keeping it exactly like that)
  • -S, --pfScale=DOUBLE — in the pf calculation, use scale*mfe as an estimate for the ensemble free energy, which helps avoid overflows 🛡️ (default=`1.07')
    • The default is 1.07, and useful values are 1.0 to 1.2. Occasionally needed for long sequences 🧬
  • --noBT — do not backtrack structures, just calculate energy contributions 🙅‍♀️ (default=off)
  • -c, --circ — assume a circular (instead of linear) RNA molecule 🔄 (default=off)

✨ 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. The placeholder file name 'DNA' can be used to load DNA parameters without 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)
    • Mostly for testing 🧪
  • --salt=DOUBLE — set the salt concentration in molar (M). Default is 1.021M 🧂

✨ Model Details ✨

Tweak the energy model and pairing rules even more with the following parameters 🎀

  • -d, --dangles=INT — how to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops 🪢 (possible values="0", "2" default=`2')
    • With -d2, dangling energies get added for the bases adjacent to a helix on both sides in any case. -d0 ignores dangling ends altogether (mostly for debugging) 🐛
  • --noGU — do not allow GU pairs 🙅 (default=off)
  • --noClosingGU — do not allow GU pairs at the end of helices 🙅‍♀️ (default=off)
  • --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 🧠

R. Lorenz, C. Flamm, I.L. Hofacker (2009), "2D Projections of RNA folding Landscapes", GI, Lecture Notes in Informatics, German Conference on Bioinformatics 2009: 157, pp 11-20 🗺️

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 ✨

I.L. Hofacker and P.F. Stadler (2006), "Memory Efficient Folding Algorithms for Circular RNA Secondary Structures", Bioinformatics 🔄

D. Adams (1979), "The hitchhiker's guide to the galaxy", Pan Books, London 🚀

Fun history moment 🧚: the mfe calculation is based on the dynamic programming algorithm originally developed by M. Zuker and P. Stiegler. The partition function algorithm is based on work by J.S. McCaskill. Iconic lineup 👑

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 👑

Ronny Lorenz 💖

🐛 REPORTING BUGS 🐛

If in doubt our program is right, nature is at fault 🌍. Comments should be sent to rna@tbi.univie.ac.at. Bestie, you've got this 🫶

That's the tea, bestie 💅 RNA2Dfold 2.7.0 · February 2026 🌸✨

📦 where this page comes from