RNAalifold
NAME
RNAalifold - calculate secondary structures for a set of aligned
RNAs
SYNOPSIS
RNAalifold [-cv weight] [-nc
weight] [-E] [-p[0]] [-C] [-T temp]
[-4] [-d] [-noLP] [-noGU] [-noCloseGU] [-e 1|2]
[-Pparamfile] [-nsp pairs]
[-S scale] [<file.aln>]
DESCRIPTION
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".
OPTIONS
- -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.
- -E
- Score pairs with endgaps same as gap-gap pairs.
- -mis
- Output "most informative sequence" instead of simple consensus:
For each column of the alignment output the set of nucleotides with
frequence greater than average in IUPAC notation.
- -p
- Calculate the partition function and base pairing probability
matrix in addition to the mfe structure. Default is calculation of
mfe structure only.
- -noLP
- 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
significant speedup.
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 filename on the command line.
CAVEATS
Since gaps are not removed for the evaluation of energies, it may
be of advantage to remove any columns with more than, say, 75% gaps
from the alignment before folding with RNAalifold.
Sequences are not weighted. If possible, do not mix very similar
and dissimilar sequences. Duplicate sequences, for example, can
distort the prediction.
SEE ALSO
The ALIDOT package http://www.tbi.univie.ac.at/RNA/ALIDOT/
REFERENCES
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,
1999
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:
1059-1066 (2002).
VERSION
This man page documents version 1.6 of the Vienna RNA Package.
AUTHORS
Ivo L Hofacker <ivo@tbi.univie.ac.at>
BUGS
If in doubt our program is right, nature is at fault. Comments
should be sent to rna@tbi.univie.ac.at.
This document was created by man2html, using the manual pages.
Time: 20:33:07 GMT, January 18, 2006