ViennaRNA (l) Return to Main Contents
RNAalifold - calculate secondary structures for a set of aligned
RNAalifold [-cv weight] [-nc
weight] [-E] [-r] [-R ribosumfile] [-old] [-mis]
[-aln] [-color] [-circ] [-p] [-C] [-T temp]
[-4] [-d] [-noLP] [-noGU] [-noCloseGU] [-e 1|2]
[-Pparamfile] [-nsp pairs]
[-S scale] [-s num] [-se num]
RNAalifold reads aligned RNA sequences from stdin or
file.aln and calculates their minimum free energy (mfe)
structure, partition function (pf) and base pairing probability
matrix. Currently, the input alignment has to be in CLUSTAL format.
It returns the mfe structure in bracket notation, its energy, the
free energy of the thermodynamic ensemble and the frequency of the
mfe structure in the ensemble to stdout. It also produces
Postscript files with plots of the resulting secondary structure
graph ("alirna.ps") and a "dot plot" of the base pairing matrix
("alidot.ps"). The file "alifold.out" will contain a list of likely
pairs sorted by credibility, suitable for viewing with "AliDot.pl".
Be warned that output file will overwrite any existing files of the
- -cv factor
- Set the weight of the covariance term in the energy function to
factor. Default is 1.
- -nc factor
- Set the penalty for non-compatible sequences in the covariance
term of the energy function to factor. Default is 1.
- Score pairs with endgaps same as gap-gap pairs.
- Output "most informative sequence" instead of simple consensus:
For each column of the alignment output the set of nucleotides with
frequency greater than average in IUPAC notation.
- Calculate the partition function and base pairing probability
matrix in addition to the mfe structure. Default is calculation of
mfe structure only. Additionally, the centroid structure is
computed and printed out.
- -MEA [gamma]
- Calculate an MEA (maximum expected accuracy) structure. See
RNAfold man page for details. If gamma is not specified a default
of gamma=1 is used. Using -MEA implies -p.
- Avoid structures without lonely pairs (helices of length 1). In
the mfe case structures with lonely pairs are strictly forbidden.
For partition function folding this disallows pairs that can
only occur isolated. Setting this option provides a
- Assume circular (instead of linear) RNA molecules.
- Produce a colored version of the consensus structure plot
"alirna.ps" (default b&w only).
- Produce a colored and structure annotated alignment in
PostScript format in the file "aln.ps" in the current
- -s num
- Compute a stochastic sample of num random structures
chosen according to their Boltzmann probability. See the -p option
- -se num
- like -s, but also print out the energy and probability
of each structure in the sample.
- -R Ribosum_Matrix
- use specified Ribosum Matrix instead of normal energy model.
Matrices to use should be 6x6 matrices, the order of the terms is
AU, CG, GC, GU, UA, UG.
- use Ribosum scoring matrix. The matrix is chosen according to
the minimal and maximal pairwise identities of the sequences in the
file. When using Ribosum scores, best benchmark results were
achieved with options -cv 0.6 -nc 0.5 (see above).
- use old energy evaluation, treating gaps as characters.
The -T, -d, -4, -noGU,
-noCloseGU, -e, -P, -nsp, options
should work as in RNAfold
If using -C constraints will be read from stdin, the
alignment has to given as a file name on the command line.
Sequences are not weighted. If possible, do not mix very similar
and dissimilar sequences. Duplicate sequences, for example, can
distort the prediction.
The ALIDOT package http://www.tbi.univie.ac.at/RNA/ALIDOT/
The algorithm is a variant of the dynamic programming algorithms of
M. Zuker and P. Stiegler (mfe) and J.S. McCaskill (pf) adapted for
sets of aligned sequences with covariance information. The energy
parameters are taken from:
D.H. Mathews, J. Sabina, M. Zuker and H. Turner "Expanded
Sequence Dependence of Thermodynamic Parameters Provides Robust
Prediction of RNA Secondary Structure" JMB, 288, pp 911-940,
If you use this program in your work you might want to cite:
Ivo L. Hofacker, Martin Fekete, and Peter F. Stadler "Secondary
Structure Prediction for Aligned RNA Sequences". J.Mol.Biol. 319:
Stephan H. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R.
Gruber, and Peter F. Stadler. "RNAalifold: Improved consensus
structure prediction for RNA alignments". BMC Bioinformatics,
This man page documents version 1.8.5 of the Vienna RNA Package.
Ivo L Hofacker <email@example.com>
If in doubt our program is right, nature is at fault.
Comments should be sent to firstname.lastname@example.org.
This document was created by man2html,
using the manual pages.
Time: 07:19:16 GMT, February 23, 2011