---
name: "RNAcalibrate"
section: "1"
platform: "linux"
package: "rnahybrid"
version: "2.1.2-8"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/RNAcalibrate"
---

# RNAcalibrate(1)

calibrate statistics of secondary structure hybridisations of RNAs

## 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

*RNAcalibrate* **is a tool for calibrating minimum free energy (mfe) hybridisations performed** **with RNAhybrid. It searches a random database that can be given on the command** **line or otherwise generates random sequences according to given sample size,** **length distribution parameters and dinucleotide frequencies. To the empirical** **distribution of length normalised minimum free energies, parameters of an** **extreme value distribution (evd) are fitted. The output gives 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. The location and scale parameters of the evd can then be given to** **RNAhybrid for the calculation of mfe p-values.**

## OPTIONS

- **-h**

  **Give a short summary of command line options.**

- **-d *frequency\_file***

  **Generate random sequences according to dinucleotide frequencies** **given in** *frequency\_file***. See example directory for example** **files.**

- **-f *from,to***

  **Forces all structures to have a helix from position** *from* **to position** *to* **with respect to the query. The first base has position 1.**

- **-k *sample\_size***

  **Generate** *sample\_size* **random sequences. Default value is 5000.**

- **-l *mean,std***

  **Generate random sequences with a normal length distribution of** **mean** *mean* **and standard deviation** *std***. Default values are 500 and** **300, respectively.**

- **-m *max\_target\_length***

  **The maximum allowed length of a target sequence. The default value is** **2000. This option only has an effect if a target file is given with the -t** **option (see below).**

- **-n *max\_query\_length***

  **The maximum allowed length of a query sequence. The default value is 30. This** **option only has an effect if a query file is given with the -q option (see** **below).**

- **-u *iloop\_upper\_limit***

  **The maximally allowed number of unpaired nucleotides in either side of an** **internal loop.**

- **-v *bloop\_upper\_limit***

  **The maximally allowed number of unpaired nucleotides in a bulge loop.**

- **-s**

  **Generate random sequences according to the dinucleotide distribution of given** **targets (either with the -t option or on command line. If no -t is given,** **either the last argument (if a -q is given) or the second last argument (if no** **-q is given) to RNAcalibrate is taken as a target). See -t option.**

- **-t *target\_file***

  **Without the -s option, each of the target sequences in** *target\_file* **is** **subject to hybridisation with each of the queries (which either are from the** *query\_file* **or is the one query given on command line; see -q below). The** **sequences in the** *target\_file* **have to be in FASTA format, ie. one line** **starting with a \> and directly followed by a name, then one or more following** **lines with the sequence itself. Each individual sequence line must not have** **more than 1000 characters.**

  **With the -s option, the target (or target file) dinucleotide distribution is** **counted, and random sequences are generated according to this distribution.**

  **If no -t is given, random sequences are generated as described above** **(see -d option).**

- **-q *query\_file***

  **See -t option above. If no -q is given, 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

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

## SEE ALSO

**RNAhybrid, RNAeffective**