Section: ViennaRNA (l)
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RNAplfold - calculate locally stable secondary structure - pair
RNAplfold [-L span] [-W winsize] [-T temp] [-4]
[-noLP] [-noGU] [-noCloseGU] [-P paramfile]
[-nsp pairs] [-d[0|2] [-c cutoff] [-o] [-u
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
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.
- -W winsize
- Average pair probabilities over windows of size winsize.
- -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.
- Save memory by printing out everything during computation.
Saves memory, and is activated per default for sequences over 1M
- -u (width)
- Compute the mean probability that regions of length 1 to
width are unpaired. Output is saved in the file name_lunp file,
where name is the name of the sequence or "plfold" if none give.
Default width is 31.
- toggles -u option, output is switched from probabilities
to free energies by taking the logarithm (note that this is not exactly the
mean breaking energy since <ln p> != ln <p>)
The -T, -d -4, -noGU,
-noCloseGU, -e, -P, -nsp, options work
as in RNAfold.
S. H. Bernhart, I.L. Hofacker, and P.F. Stadler (2006) "Local Base
Pairing Probabilities in Large RNAs" Bioinformatics 22: 614-615
A.F. Bompfünewerer, R. Backofen, S.H. Bernhart, J.
Hertel, I.L. Hofacker, P.F. Stadler, S. Will (2008) "Variations on
RNA Folding and Alignment: Lessons from Benasque" J. Math. Biol. 56:119–144
This man page documents version 1.8 Vienna RNA Package.
Stephan H Bernhart, Ivo L Hofacker, Peter F Stadler.
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Time: 09:18:51 GMT, September 02, 2008