RNADOS(1)

Okay bestie, welcome to the RNADOS(1) page 🎀 (it's a User Commands icon 💅), all about the RNAdos tool, and I'm about to make it make sense 🫶

✨ NAME ✨

RNAdos 💖 manual page for RNAdos 2.7.0 🌸

✨ SYNOPSIS ✨

RNAdos [OPTIONS]

Literally one line. The whole vibe is "throw options at it" 💅

✨ DESCRIPTION ✨

RNAdos 2.7.0 🦋 the version drop!

So the main job is to calculate the density of states for each energy band of an RNA 🧬✨ It reads an RNA sequence and computes the density of states for each energy band. Iconic 👑

Here are the options, slay them all:

• -h, --help — print help and exit 🙈
• --detailed-help — print help, including all the details and hidden options, then exit 🧚
• --full-help — print help, including hidden options, then exit
• -V, --version — print the version and exit 🌈
• -v, --verbose — be verbose 📣 (default=off)
  • Lowers the log level so even INFO messages get passed through 🫧

I/O Options 📥

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

• -s, --sequence=STRING — the RNA sequence, written with ACGU 🧬
• -j, --numThreads=INT — sets how many threads do the calculations 🔥 (only available when compiled with OpenMP support)
• --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 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=`RNAdos.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)

Algorithms 🧠

Pick extra algorithms to include in the calculations. The Minimum free energy (MFE) and a structure representative are calculated in any case, no cap 🫶

• -e, --max-energy=INT — structures only get counted until this threshold is reached. Default is 0 kcal/mol. (default=`0')
• -b, --hashtable-bits=INT — sets the size of the hash table for each cell in the dp-matrices 🧺 (default=`20')

Energy Parameters ⚡

Energy parameter sets can be adapted or loaded from user-provided input files 📂

• -T, --temp=DOUBLE — rescales energy parameters to a temperature of temp C. Default is 37C 🌡️ (default=`37.0')
• -P, --paramFile=paramfile — reads energy parameters from paramfile instead of using the default set 🎀
  • Different sets of energy parameters for RNA and DNA should come with your distribution. See the RNAlib documentation for the file format details. The placeholder file name 'DNA' lets you load DNA parameters without actually specifying any input file 🧚
• --salt=DOUBLE — sets the salt concentration in molar (M). Default is 1.021M 🧂

Model Details 🎀

Tweak the energy model and pairing rules even more with these 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, that 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 works only for mfe folding 🫠
  • Note that with -d1 and -d3, only the MFE computations use this setting, while partition function uses the -d2 setting. So dangling ends get treated differently, bestie 👀
• --helical-rise=FLOAT — sets 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 — sets 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 lowkey iconic papers 🌸

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

J. Cupal, I.L. Hofacker, P.F. Stadler (1996), "Dynamic programming algorithm for the density of states of RNA secondary structures" Computer Science and Biology 96, Proc. German Conf. on Bioinformatics 1996, pp. 184-186.

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 👑

Gregor Entzian, 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.

🔗 SEE ALSO 🔗

RNAsubopt(1) 🦋

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That's the whole tea ☕ RNAdos 2.7.0, dropped February 2026, straight from the RNADOS(1) files. Stay iconic 💅🌈