RNADISTANCE(1)

Okay bestie, let's get into the RNAdistance manual 💖

✨ NAME ✨

RNAdistance — manual page for RNAdistance 2.7.0 🎀

💅 SYNOPSIS 💅

RNAdistance [OPTION]...

🦋 DESCRIPTION 🦋

RNAdistance 2.7.0 🌸

Calculate distances between RNA secondary structures ✨

okay so RNAdistance reads RNA secondary structures from stdin and calculates one or more measures of how different they are. It's based on tree or string editing (alignment), and it's giving precision 💅 It also calculates a "base pair distance", which is the number of base pairs that show up in one structure but not the other. ngl, base pair distance isn't recommended for structures of different lengths 🙈

RNAdistance takes structures in bracket format, where matching brackets are base pairs and unpaired bases are a dot .. You can also use coarse grained representations, where hairpins, interior loops, bulges, multiloops, stacks and external bases are written as (H), (I), (B), (M), (S) and (E). These can be weighted too 💜 Full structures can be written the same way using (U) for unpaired bases and (P) for paired bases. This is the HIT representation (you don't want to know what this means 💀). For example, this structure has 2 hairpins joined by a multiloop:

  .((..(((...)))..((..)))).       full structure (usual format);
  (U)((U2)((U3)P3)(U2)((U2)P2)P2) HIT structure;
  ((H)(H)M)  or
  ((((H)S)((H)S)M)S)              coarse grained structure;
  (((((H3)S3)((H2)S2)M4)S2)E2)    weighted coarse grained.

The program keeps reading new structures until it hits a line with just the single character @, or an end of file. Input lines that aren't a valid structure and don't start with > get ignored, so no drama 🫶

• -h, --help — Print help and exit 🌷
• --detailed-help — Print help with 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. The default is off 🎀

Lowers the log level so even INFO messages get through 📣

• -D, --distance=fhwcFHWCP — Pick the distance representation you want to use in the calculations. The default is f ✨

Use the full, HIT, weighted coarse, or coarse representation to calculate the distance. Capital letters mean string alignment, otherwise tree editing is used. You can mix and match any combination of distances 🦋

• -X, --compare=p|m|f|c — Set the comparison directive. The default is p 👑

These are the possible arguments for this option:

• -Xp — compare the structures pairwise (p), so first with 2nd, third with 4th, and so on 💖
• -Xm — calculate the distance matrix between all structures. The output is formatted as a lower triangle matrix 🔺
• -Xf — compare each structure to the first one 🫶
• -Xc — compare continuously, so the i-th structure with the (i+1)th structure 🌈

• -S, --shapiro — Use Bruce Shapiro's cost matrix for comparing coarse structures. Default is off 🍓
• -B, --backtrack[=<filename>] — Print an "alignment" with gaps in the structures so you can see the matching substructures 🔎 The default is none.

If you don't give a <filename>, the output goes to stdout, unless -Xm is set. In that case it's written to "backtrack.file" 📂 If you do give <filename>, the aligned structures get written there.

• --log-level=level — Set the log level threshold. The default is 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 everything, even errors and other critical info 🙈

• --log-file[=filename] — Print log messages to a file instead of stderr. The default filename is RNAdist.log 📝
• --log-time — Include a time stamp in log messages. Default is off ⏰
• --log-call — Include the file and line of the log calling function. Default is off 🕵️‍♀️

📚 REFERENCES 📚

If you use this program in your work, you might wanna 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 ✨

B.A. Shapiro (1988), "An algorithm for comparing multiple RNA secondary structures" CABIOS: 4, pp 381-393 🦋

B.A. Shapiro, K. Zhang (1990), "Comparing multiple RNA secondary structures using tree comparison", CABIOS: 6, pp 309-318 💅

W. Fontana, D.A.M. Konings, P.F. Stadler and P. Schuster P (1993), "Statistics of RNA secondary structures", Biopolymers: 33, pp 1389-1404 🌈

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 👑

Walter Fontana, Ivo L Hofacker, Peter F Stadler 🫶

🙈 REPORTING BUGS 🙈

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

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That's the whole tea, bestie 🧚 RNAdistance 2.7.0, February 2026, RNADISTANCE(1) 💜