RNACALIBRATE(1)

💖 RNAcalibrate 💖

okay bestie, welcome to RNAcalibrate from the General Commands Manual ✨ this is the page where I spill the whole tea so you can stop guessing 🫶

✨ NAME ✨

RNAcalibrate - calibrate statistics of secondary structure hybridisations of RNAs 🧬

✨ SYNOPSIS ✨

RNAcalibrate [-h] [-d frequency_file] [-f from,to] [-k sample_size] [-l
mean,std] [-m max_target_length] [-n max_query_length] [-u
iloop_upper_limit] [-v bloop_upper_limit] [-s] [-t target_file] [-q
query_file] [target] [query]

✨ DESCRIPTION ✨

okay so RNAcalibrate is the calibration queen for minimum free energy (mfe) hybridisations done with RNAhybrid 👑 it digs through a random database, which you can hand over on the command line. if you don't, it just makes random sequences based on your sample size, length distribution parameters and dinucleotide frequencies 🎀

then it fits an extreme value distribution (evd) to the empirical distribution of length normalised minimum free energies 💅 the output is giving: for each miRNA, its name (or "command_line" if it was submitted on the command line), the number of data points the evd fit was done on, the location and the scale parameter 🦋

and the vibe check: you can feed those location and scale parameters of the evd into RNAhybrid so it can calculate mfe p-values ✨

✨ OPTIONS ✨

• -h — the quick cheat sheet. it gives you a short summary of the command line options 📝
• -d frequency_file — makes random sequences that follow the dinucleotide frequencies in frequency_file. check the example directory for example files 📁
• -f from,to — forces every structure to have a helix running from position from to position to, counted against the query. the first base is position 1 🎀
• -k sample_size — generates sample_size random sequences. the default is 5000 🌸
• -l mean,std — makes random sequences with a normal length distribution, where mean is the mean and std is the standard deviation. the defaults are 500 and 300, respectively (so mean 500 and std 300) 🍓
• -m max_target_length — the longest a target sequence is allowed to be. default is 2000. this only matters if you give a target file with -t (more on that below) 🧚
• -n max_query_length — the longest a query sequence is allowed to be. default is 30. this only does something if you give a query file with -q (also more below) 💜
• -u iloop_upper_limit — the max number of unpaired nucleotides allowed on either side of an internal loop 🌈
• -v bloop_upper_limit — the max number of unpaired nucleotides allowed in a bulge loop ⭐
• -s — generates random sequences that follow the dinucleotide distribution of your targets (given either with -t or on the command line). if there's no -t, the last argument (when -q is given) or the second last argument (when there's no -q) to RNAcalibrate gets treated as a target. see -t 🫧
• -t target_file — okay, this one has a lot of tea:
  • without -s, each target sequence in target_file gets hybridised with each query. the queries come from the query file or the one query you put on the command line (see -q). the sequences in target_file have to be in FASTA format, meaning a 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 🚫
  • with -s, the dinucleotide distribution of the target (or target file) gets counted, and random sequences are generated according to that distribution 📊
  • if there's no -t, random sequences are generated as described above (see -d) 🎲
• -q query_file — see -t above. if there's no -q, the last argument to RNAcalibrate is taken as a query 💖

✨ REFERENCES ✨

the energy parameters are taken from:

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 📚

✨ VERSION ✨

this man page documents version 2.0 of RNAcalibrate 🏷️

✨ AUTHORS ✨

Marc Rehmsmeier, Peter Steffen, Matthias Hoechsmann 🫶

✨ LIMITATIONS ✨

⚠️ bestie, heads up: character dependent energy values are only defined for [acgtuACGTU]. every other character leads to a value of zero in these cases 💀

✨ SEE ALSO ✨

RNAhybrid, RNAeffective 🔥

and that's the whole page, bestie 💜 the footer says RNACALIBRATE(1) ✨ slay 💅