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.