# RNAPLFOLD

ViennaRNA (l) Return to Main Contents

## NAME

RNAplfold - calculate locally stable secondary structure - pair
probabilities
## SYNOPSIS

**RNAplfold** [-L span] [-W winsize] [-T *temp*] [-4]
[-noLP] [-noGU] [-noCloseGU] [-P *paramfile*]
[-nsp *pairs*] [-d[0|2] [-c *cutoff*] [-o] [-u
*number of unpaired*] [-O]
## DESCRIPTION

*RNAplfold* computes local pair probabilities for base pairs
with a maximal span of L. The probabilities are averaged over all
windows of size L that contain the base pair. For a sequence of
length n and a window size of L the algorithm uses only O(n+L*L)
memory and O(n*L*L) CPU time. Thus it is practical to "scan" very
large genomes for short stable RNA structures.
Output consists of a dot plot in postscript file, where the
averaged pair probabilities can easily be parsed and visually
inspected.

The -u option makes i possible to compute the probability that a
stretch of x consequtive nucleotides is unpaired, which is useful
for predicting possible binding sites. Again this probability is
averaged over all windows containing the region.

**WARNING! Output format changed!!**

The output is a plain text matrix containing on each line a
position i followed by the probability that i is unpaired, [i-1..i]
is unpaired [i-2..i] is unpaired and so on to the probability that
[i-x+1..i] is unpaired.

## OPTIONS

**-W winsize**
- Average pair probabilities over windows of size
*winsize*.
Default 70.

**-L span**
- Allow only pairs (i,j) with j-i<=span. Default winSize.

**-c cutoff**
- Report only base pairs with an average probability >
*cutoff* in the dot plot; default=0.01.

**-o**
- Save memory by printing out everything during computation.
Saves memory, and is activated per default for sequences over 1M
bp.

**-u (width)**
- Compute the mean probability that regions of length 1 to
*width* are unpaired. Output is saved in a _lunp file. Default
width is 31.

**-O**
- toggles
**-u** option, output is switched from probabilities
to their logarithm, which are NOT exactly the mean energies needed
to the respective stretch of bases!

The **-T**, **-d** **-4**, **-noGU**,
**-noCloseGU**, **-e**, **-P**, **-nsp**, options work
as in RNAfold.

## SEE ALSO

RNALfold(1)
## REFERENCES

S. H. Bernhart, I.L. Hofacker, and P.F. Stadler (2006) "Local Base
Pairing Probabilities in Large RNAs" Bioinformatics 22: 614-615

A.F. BompfÃ¼newerer, R. Backofen, S.H. Bernhart, J.
Hertel, I.L. Hofacker, P.F. Stadler, S. Will (2007) "Variations on
{RNA} Folding and Alignment: Lessons from Benasque" J. Math. Biol.
## VERSION

This man page documents version 1.6 Vienna RNA Package.
## AUTHORS

Stephan H Bernhart, Ivo L Hofacker, Peter F Stadler.

Send comments to <rna@tbi.univie.ac.at>

This document was created by man2html,
using the manual pages.

Time: 07:19:16 GMT, February 23, 2011