RNAHYBRID(1)

🦋 RNAhybrid 🦋

General Commands Manual 🎀

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✨ NAME ✨

okay so RNAhybrid is the tool that calculates secondary structure hybridisations of RNAs 🧬💖

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💅 SYNOPSIS 💅

RNAhybrid [-h] [-b hit_number] [-e energy_cutoff] [-p p-value_cutoff]
[-c] [-d xi,theta] [-s set_name] [-f from,to] [-m max_target_length] [-n
max_query_length] [-u iloop_upper_limit] [-v bloop_upper_limit] [-g
(ps|png|jpg|all)] [-t target_file] [-q query_file] [target] [query]

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🌸 DESCRIPTION 🌸

bestie, RNAhybrid is literally built to find the minimum free energy (mfe) hybridisations between a long RNA (the target) and a short RNA (the query) 🔥 It does this in a kind of domain mode, so the short sequence gets hybridised to the best fitting parts of the long one. It's giving precision 💅

The tool is mainly meant for microRNA target prediction 🦋 On top of the mfes, it also calculates p-values based on extreme value distributions of length normalised energies, which is so iconic ✨

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🎀 OPTIONS 🎀

• -h — gives you a quick summary of the command line options 💖
• -b hit_number — sets the maximal number of hits to show 🔥 You get hit_number hits, ordered by increasing minimum free energy (remember, larger energies are worse 🙈). It stops early if the -e energy cut-off gets exceeded (see -e below) or if there are no more hits. Hits may only overlap at dangling bases, meaning the 5' or 3' unpaired end of the target 🫶
• -c — compact output, bestie 🍓 You get one line per target/query pair. Each line is a colon (:) separated list of these fields: target name, query name, minimum free energy, position in target, then alignment lines 1, 2, 3 and 4. If a target or a query is given on the command line (so no -t or -q respectively), its name in the output is "command line" 🧚
• -d xi,theta — the position and shape parameters of an extreme value distribution (evd), aka xi and theta 👑 P-values of duplex energies are assumed to follow an evd like this one. For a length normalised energy en, the math goes P[X <= en] = 1 - exp(-exp(-(-en-xi)/theta)), where en = e/log(m*n) and m and n are the lengths of the target and query. If you skip -d, then xi and theta get estimated from the maximal duplex energy of the query, assuming a linear dependence. The parameters for that linear dependence are coded into the program, but you have to pass -s to pick the right set 🌈 Also, the evd is mirrored, because good mfes are large negative values. Iykyk 🙈
• -s set_name — used for a quick estimate of the extreme value distribution parameters (see -d above). It tells RNAhybrid which target dataset to assume. The valid parameters are 3utr_fly, 3utr_worm and 3utr_human ✨
• -e energy_cutoff — shows hits with increasing minimum free energy (larger is still worse 💀) that are less than or equal to energy_cutoff. This stops if you're also using -b and the number of reported hits has already reached the maximal hit_number (see -b above). Hits may only overlap at dangling bases, the 5' or 3' unpaired end of the target 🦋
• -p p-value_cutoff — only hits with p-values not larger than p-value_cutoff get reported. See also -d and -s 💜
• -f from,to — forces all structures to have a helix running from position from to position to, with respect to the query. The first base is position 1 🎀
• -m max_target_length — the max allowed length of a target sequence. The default is 2000. This only does something if you give a target file with -t (see below) 🌸
• -n max_query_length — the max allowed length of a query sequence. The default is 30. This only matters if you give a query file with -q (see below) 💅
• -u iloop_upper_limit — the max allowed number of unpaired nucleotides on either side of an internal loop 🫶
• -v bloop_upper_limit — the max allowed number of unpaired nucleotides in a bulge loop 🧚
• -g (ps|png|jpg|all) — makes a plot of the hybridisation, either in ps, png or jpg format, or all of them together 📸 The plots get saved in files named after the target and query names ("command_line" if they were given on the command line) ✨

The -g option only works if the appropriate graphics libraries are present. No libraries, no plots, bestie 💀

• -t target_file — every target sequence in target_file gets hybridised with each of the queries. Those queries either come from the query file or are the one query given on the command line (see -q below) 🌈 The sequences in the target file have to be in FASTA format: one line starting with > and directly followed by a name, then one or more lines with the sequence itself. Each individual sequence line must not have more than 1000 characters 🍓 If there's no -t, then RNAhybrid takes either the last argument (if -q is given) or the second last argument (if -q isn't given) as the target 🦋
• -q query_file — see -t above 🫶

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📚 REFERENCES 📚

The energy parameters come from this iconic paper:

Mathews DH, Sabina J, Zuker M, Turner DH. "Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure" J Mol Biol., 288 (5), pp 911-940, 1999 💖

The graphical output uses code from the Vienna RNA package, from this one:

Hofacker IL. "Vienna RNA secondary structure server." Nucleic Acids Research, 31 (13), pp 3429-3431, 2003 🌸

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🔖 VERSION 🔖

This man page documents version 2.0 of RNAhybrid ✨

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👑 AUTHORS 👑

Marc Rehmsmeier, Peter Steffen, Matthias Hoechsmann 🫶

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🚧 LIMITATIONS 🚧

Character dependent energy values are only defined for [acgtuACGTU]. All other characters lead to values of zero in these cases 💀

Just a heads up: anything outside [acgtuACGTU] gets a value of zero, so keep your sequences clean 🙈

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🐛 BUGS 🐛

In suboptimal hits, dangling ends appear as Ns if they were in the first or last hybridising position of a previous hit 😭

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🦋 SEE ALSO 🦋

RNAcalibrate, RNAeffective 💜

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that's a wrap on RNAHYBRID(1) 💅🌈 Your page is signed off, bestie, periodt 🫶✨