RNASNOOP(1)

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

✨ RNASNOOP(1) ✨

🎀 NAME 🎀

RNAsnoop 💖 manual page for RNAsnoop 2.7.0

🦋 SYNOPSIS 🦋

RNAsnoop [options]

📖 DESCRIPTION 📖

RNAsnoop 2.7.0 🌸

Find targets of a query H/ACA snoRNA ✨

okay so RNAsnoop reads a target RNA sequence and a H/ACA snoRNA sequence from a target and query file, respectively, and then computes optimal and suboptimal secondary structures for their hybridization 💅. The calculation can be done roughly in O(nm), where n is the length of the target sequence and m is the length of the snoRNA stem. It's literally tailored to the special case of H/ACA snoRNA, so it's giving specialist energy 🔥. For general purpose target predictions, bestie, go look at RNAduplex, RNAup, RNAcofold and RNAplex 🫶. Accessibility effects can be estimated by RNAsnoop if a RNAplfold accessibility profile is provided 🧚.

The computed optimal and suboptimal structures get written to stdout, one structure per line 🍓. Each line consists of: the structure in dot bracket format, with a & separating the two strands 💜. The <> brackets represent snoRNA intramolecular interactions, while the () brackets represent intermolecular interactions between the snoRNA and its target 🌈.

Then you get the range of the structure in the two sequences, in the format from,to : from,to ✨, plus the energy of the duplex structure in kcal/mol 💀. If it's available, the opening energy is also returned 🙈.

  • --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 🎀
  • --verbose — Be verbose. Lowers the log level setting so even INFO messages get passed through 📣
    • default: off

🌷 I/O Options 🌷

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

  • -s, --query=STRING — File containing the query sequence. Input sequences can be piped to RNAsnoop or given in a query file with the -s option. Heads up: the -s option implies that the -t option is also used 💅.
  • -t, --target=STRING — File containing the target sequence. Input sequences can be piped to RNAsnoop or given in a target file with the -t option. Note that the -t option implies that the -s option is also used 🫶.
  • -S, --suffix=STRING — Specify the suffix that was added by RNAup to the accessibility files 🦋.
    • default: _u1_to_30.out
  • -P, --from-RNAplfold=STRING — Specify the directory where the accessibility profiles generated by RNAplfold are found 📂.
  • -U, --from-RNAup=STRING — Specify the directory where the accessibility profiles generated by RNAup are found 📁.
  • -O, --output_directory=STRING — Set where the generated figures should be stored 🖼️.
    • default: `./'
  • --log-level=level — Set the log level threshold 📝.
    • default: 2
    • By default, log messages are 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: RNAsnoop.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 🧪

Options which alter the computing behaviour of RNAplex. Please note that the options that filter out snoRNA-RNA duplexes expect the energy to be given in decacal/mol instead of kcal/mol. A threshold of -2.8(kcal/mol) should be given as -280(decacal/mol) 💅.

  • -A, --alignment-mode — Specify whether RNAsnoop gets alignments or single sequences as input 🧬.
    • default: off
  • -f, --fast-folding=INT — Speedup of the target search 🏃‍♀️.
    • default: 1
    • This option decides whether the backtracking happens (-f 1) or not (-f 0). With -f 1 the structure is computed based on the standard energy model. This is the slowest mode of RNAsnoop 🐢. -f 0 is the fastest mode, since no structures get recomputed and only the interaction energy is returned ⚡.
  • -c, --extension-cost=INT — Cost to add to each nucleotide in a duplex 💸.
    • default: 0
    • This is the cost of extending a duplex by one nucleotide. It lets you find compact duplexes with few or small bulges or internal loops 🫧. It's only useful when no accessibility profiles are available, and it's disabled if accessibility profiles are used (-P option) 🚫.
  • -e, --energy-threshold=DOUBLE — Maximal energy difference between the mfe and the desired suboptimal 🎯.
    • default: -1
    • This is the energy range for a duplex to be returned. The threshold is set on the total energy of interaction, meaning the hybridization energy corrected for opening energy if -a is set, or the energy corrected by -c. If it's unset, only the mfe gets returned 🥀.
  • -o, --minimal-right-duplex=INT — Minimal Right Duplex Energy 👉.
    • default: -270
  • -l, --minimal-loop-energy=INT — Minimal Right Duplex Energy. Yes, that's the label the page itself uses, bestie 💀.
    • default: -280
    • This is the minimal stem loop energy of the snoRNA. The energy should be given in decacalories, so a minimal stem-loop energy of -2.8 kcal/mol corresponds to -280 decacal/mol 🧮.
  • -p, --minimal-left-duplex=INT — Minimal Left Duplex Energy 👈.
    • default: -170
  • -q, --minimal-duplex=INT — Minimal Duplex Energy 🧷.
    • default: -1090
  • -d, --duplex-distance=INT — Distance between the target 3' ends of two consecutive duplexes 📏.
    • default: 2
    • This should be set to the maximal length of interaction to get good results 🎀. A smaller d leads to larger overlaps between consecutive duplexes 🍰.
  • -h, --minimal-stem-length=INT — Minimal snoRNA stem length 🌱.
    • default: 5
  • -i, --maximal-stem-length=INT — Maximal snoRNA stem length 🌳.
    • default: 120
  • -j, --minimal-duplex-box-length=INT — Minimal distance between the duplex end and the H/ACA box 📦.
    • default: 11
  • -k, --maximal-duplex-box-length=INT — Maximal distance between the duplex end and the H/ACA box 🎁.
    • default: 16
  • -m, --minimal-snoRNA-stem-loop-length=INT — Minimal number of nucleotides between the beginning of the stem loop and the beginning of the snoRNA sequence 🔁.
    • default: 1
  • -n, --maximal-snoRNA-stem-loop-length=INT — Maximal number of nucleotides between the beginning of the stem loop and the beginning of the snoRNA sequence 🔂.
    • default: 100000
  • -v, --minimal-snoRNA-duplex-length=INT — Minimal distance between the duplex start and the snoRNA 🧭.
    • default: 0
  • -w, --maximal-snoRNA-duplex-length=INT — Maximal distance between the duplex start and the snoRNA 🗺️.
    • default: 0
  • -x, --minimal-duplex-stem-energy=INT — Minimal duplex stem energy 💫.
    • default: -1370
  • -y, --minimal-total-energy=INT — Minimal total energy 🔋.
    • default: 100000
  • -a, --maximal-stem-asymmetry=INT — Maximal snoRNA stem asymmetry ⚖️.
    • default: 30
  • -b, --minimal-lower-stem-energy=INT — Minimal lower stem energy 🛏️.
    • default: 100000
  • -L, --alignmentLength=INT — Limit the extent of the interactions to L nucleotides 📐.
    • default: 25

🎀 Structure Constraints 🎀

Command line options to interact with the structure constraints feature of this program 🧩

  • -C, --constraint — Calculate the stem structure subject to constraints 🔒.
    • default: off
    • The program reads the stem sequence first, then a string containing constraints on the structure, encoded with these symbols:
      • . — no constraint for this base 🫥
      • | — the corresponding base has to be paired 💞
      • x — the base is unpaired 🙅‍♀️
      • < — base i is paired with a base j>i ➡️
      • > — base i is paired with a base j<i ⬅️
      • matching brackets ( ) — base i pairs base j 🤝
    • With the exception of |, constraints will disallow all pairs that conflict with the constraint. This is usually enough to enforce the constraint, but occasionally a base may stay unpaired in spite of constraints 😭. PF folding ignores constraints of type | 🙈.

🌈 Plotting 🌈

Command line options for changing the default behaviour of structure layout and pairing probability plots 🎨

  • -I, --produce-ps — Draw annotated 2D structures for a list of dot-bracket structures 🖍️.
    • default: off
    • This option lets you produce interaction figures in PS-format with conservation/accessibility annotation, if that's available 🧁.
  • -N, --direct-redraw — Outputs 2D interactions concurrently with the interaction calculation for each suboptimal interaction. Honestly, the -I option should be preferred 💅.
    • default: off

(continued in part 2 🦋)

✨ AUTHOR ✨

okay bestie, the credits 🎀 Hakim Tafer and Ivo L. Hofacker are the ones who built this, and they're literally the reason we get to be this good at RNA 🧬💅

🐛 REPORTING BUGS 🐛

okay so the vibe here is: if in doubt our program is right, nature is at fault 💀🙈 like, the code is not the problem, the RNA is being extra 😭

if you find a bug, send your comments to rna@tbi.univie.ac.at 💌 that's the spot 🫶

that's the whole contact info, so don't go looking for a different address 🌸

RNAsnoop 2.7.0 ✨ February 2026 ✨ RNASNOOP(1) 🦋

bestie, that's the official footer 💜 we're living in the RNAsnoop 2.7.0 era, and this page was last updated February 2026, so you're literally reading the freshest tea 🍓 periodt 💅

📦 where this page comes from