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

# RNAeffective(1)

calculation of effective numbers of orthologous miRNA targets

## NAME

RNAeffective - calculation of effective numbers of orthologous miRNA targets

## SYNOPSIS

**RNAeffective \[-h\] \[-d** *frequency\_file***\] \[-f** *from,to***\] \[-k** *sample\_size***\] \[-l** *mean,std***\] \[-m** *max\_target\_length***\] \[-n** *max\_query\_length***\] \[-u** *iloop\_upper\_limit***\] \[-v** *bloop\_upper\_limit***\] \[-s\] \[-t** *target\_file***\] \[-q** *query\_file***\]** **\[***query***\]**

## DESCRIPTION

*RNAeffective* **is a tool for determining the effective number of orthologous miRNA targets.** **This number can be used for the calculation of more accurate joint p-values in** **multi-species analyses. RNAeffective searches a set of target sequences with** **random miRNAs that can be given on the command line or otherwise generates** **random sequences according to given sample size, length distribution parameters** **and dinucleotide frequencies. The empirical distribution of joint p-values is** **compared to the p-values themselves, and the effective number of independent** **targets is the one that reduces the deviation between the two distributions.**

## 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 22 and** **0, 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** **queries (either with the -q option or on command line. If no -q is given,** **the last argument to RNAeffective is taken as a query). See -q option.**

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

  **Without the -s option, each of the query sequences in** *query\_file* **is** **subject to hybridisation with each of the targets (which are from the** *target\_file***; see -t below). The sequences in the** *query\_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 query (or query file) dinucleotide distribution is** **counted, and random sequences are generated according to this distribution.**

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

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

  **See -q 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**

## VERSION

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

## 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, RNAcalibrate**