CT2DB(1)

💖 CT2DB — the ct2db manual, but make it a group chat 💖

okay bestie, sit down, hydrate, because we're about to talk about ct2db 💅 this is the 2.7.0 era and we're thriving.

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✨ NAME ✨

ct2db — literally the manual page for ct2db 2.7.0. that's it. that's the name. iconic of her honestly.

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🌸 SYNOPSIS 🌸

ct2db [OPTIONS] [<input0.ct>] [<input1.ct>]...

yes she takes multiple inputs. main character energy fr fr 🦋

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🎀 DESCRIPTION 🎀

so ct2db is 2.7.0, okay, and what she does is produce dot bracket notation of an RNA secondary structure from Zuker's .ct file. no cap.

basically: this program converts connectivity table (.ct) files into extended FASTA format with a dot-bracket string. that's the whole vibe. she reads your .ct, she hands you back pretty little dots and brackets, and honestly? obsessed. 🌈

and here are all her lil switches, every single one, no skipping, i promised:

• -h, --help — print help and dip. that's it, that's the whole thing 💖
• --detailed-help — print help but with ALL the details and the hidden options too, then exit. the director's cut. 🎬
• --full-help — print help including the hidden options, then exit. (yes, slightly different from the above, don't come for me, that's just what it says 👑)
• -V, --version — print version and exit. she'll tell you who she is ✨
• -p, --no-pk — remove pseudoknots from structure. bye bye pseudoknots 💀 (default = off)
• -m, --no-modified — do not keep modified bases, i.e. replace all non-canonical nucleotides with N. (default = off)
• -v, --verbose — be verbose. she will talk. (default = off)
• --log-level=level — set log level threshold. (default = 2)

okay so this one needs a lil moment 🫶 by default, any log messages get filtered such that only warnings (level 2) or errors (level 3) are printed. this setting lets you specify the log level threshold, where higher values result in fewer information. and listen — log-level 5 turns off all messages, even errors and other critical information. so like, be careful with that one bestie, she will go completely silent on you 😭

• --log-file[=filename] — print log messages to a file instead of stderr. (default = ct2db.log) 📝
• --log-time — include time stamp in log messages. (default = off) ⏰
• --log-call — include file and line of log calling function. (default = off) 🔍

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🦋 REFERENCES 🦋

if you use this program in your work you might want to cite — and like, you should, it's the polite thing to do, give them their flowers 🌸:

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

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💀 REPORTING BUGS 💀

okay the energy here is unmatched, i need you to read it exactly as written:

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

literally if in doubt our program is right, nature is at fault. periodt. 💅 if you got thoughts, comments, feelings, a bug, a love letter — send it to rna@tbi.univie.ac.at. they're listening 🫶

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and that's the whole page bestie!! 🎀 this was ct2db 2.7.0, dated February 2026, from the User Commands section of the manual — go forth, convert your .ct files, and slay ✨👑🌈