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

# RNAhybrid(1)

calculate secondary structure hybridisations of RNAs

## NAME

RNAhybrid - calculate secondary structure hybridisations of RNAs

## SYNOPSIS

**RNAhybrid \[-h\] \[-b** *hit\_number***\] \[-e** *energy\_cutoff***\] \[-p** *p-value\_cutoff***\] \[-c\] \[-d** *xi,theta***\] \[-s** *set\_name***\] \[-f** *from,to***\] \[-m** *max\_target\_length***\] \[-n** *max\_query\_length***\] \[-u** *iloop\_upper\_limit***\] \[-v** *bloop\_upper\_limit***\] \[-g (ps\|png\|jpg\|all)\]** **\[-t** *target\_file***\] \[-q** *query\_file***\] \[***target***\] \[***query***\]**

## DESCRIPTION

*RNAhybrid* **is a tool for finding minimum free energy (mfe) hybridisations of a long** **(target) and a short (query) RNA. The hybridisation is performed in a kind of** **domain mode, ie. the short sequence is hybridised to the best fitting parts of** **the long one. The tool is primarily meant as a means for microRNA target** **prediction.  In addition to mfes, the program calculates p-values based on** **extreme value distributions of length normalised energies.**

## OPTIONS

- **-h**

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

- **-b *hit\_number***

  **Maximal number of hits to show.** *hit\_number* **hits with increasing minimum** **free energy (reminder: larger energies are worse) are shown, unless the -e** **option is used and the energy cut-off has been exceeded (see -e option below) or** **there are no more hits. Hits may only overlap at dangling bases (5' or 3'** **unpaired end of target).**

- **-c**

  **Produce compact output. For each target/query pair one line of output** **is generated. Each line is a colon (:) separated list of the following** **fields: target name, query name, minimum free energy, position in target,** **alignment line 1, line 2, line 3, line 4. If a target or a query is given** **on command line (ie. no -t or -q respectively), its name in the output** **will be "command line".**

- **-d *xi,theta***

  **xi and theta are the position and shape parameters, respectively, of an extreme** **value distribution (evd). p-values of duplex energies are assumed to be** **distributed according to such an evd. For a length normalised energy en, we** **have P\[X \<= en\] = 1 - exp(-exp(-(-en-xi)/theta)), where en = e/log(m\*n) with m** **and n being the lengths of the target and the query, respectively. If the -d** **option is omitted, xi and theta are estimated from the maximal duplex energy of** **the query, assuming a linear dependence. The parameters of this linear** **dependence are coded into the program, but the option -s has to be given to** **choose from the appropriate set. Note that the evd is mirrored, since good mfes** **are large negative values.**

- **-s *set\_name***

  **Used for quick estimate of extreme value distribution parameters (see -d** **option above). Tells RNAhybrid which target dataset to assume. Valid parameters** **are 3utr\_fly, 3utr\_worm and 3utr\_human.**

- **-e *energy\_cutoff***

  **Hits with increasing minimum free energy (reminder: larger energies are worse)** **less than or equal to** *energy\_cutoff* **are shown, unless the -b option is** **used and the number of already reported hits has reached the maximal** *hit\_number* **(see -b option above). Hits may only overlap at dangling** **bases (5' or 3' unpaired end of target).**

- **-p *p-value\_cutoff***

  **Only hits with p-values not larger than** *p-value\_cutoff* **are reported.** **See also options -d and -s.**

- **-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.**

- **-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.**

- **-g (ps\|png\|jpg\|all)**

  **Produce a plot of the hybridisation, either in ps, png or jpg format,** **or for all formats together. The plots are saved in files whose names are** **created from the target and query names ("command\_line" if given on the** **command line). This option only works, if the appropriate graphics libraries** **are present.**

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

  **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. 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 RNAhybrid is taken as a** **target.**

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

  **See -t option above.**

## 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**

**The graphical output uses code from the Vienna RNA package:**

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

## VERSION

**This man page documents version 2.0 of RNAhybrid.**

## 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.**

## BUGS

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

## SEE ALSO

**RNAcalibrate, RNAeffective**