RNAfold man page
RNAfold - calculate secondary structures of RNAs
SYNOPSIS
RNAfold [-p[0]] [-C] [-T temp] [-4] [-d[0|1|2|3]] [-noLP] [-noGU] [-noCloseGU] [-e 1|2] [-P paramfile] [-nsp pairs] [-S scale] [-circ]DESCRIPTION
RNAfold reads RNA sequences from stdin, calculates their minimum free energy (mfe) structure and prints to stdout the mfe structure in bracket notation and its free energy. If the -p option was given it also computes the partition function (pf) and base pairing probability matrix, and prints the free energy of the thermodynamic ensemble, the frequency of the mfe structure in the ensemble, and the ensemble diversity to stdout.It also produces PostScript files with plots of the resulting
secondary structure graph and a "dot plot" of the base pairing
matrix. The dot plot shows a matrix of squares with area
proportional to the pairing probability in the upper half, and one
square for each pair in the minimum free energy structure in the
lower half. For each pair i-j with probability p>10E-6 there is
a line of the form
i j sqrt(p) ubox
in the PostScript file, so that the pair probabilities can be
easily extracted. If the sequence is preceded by a line of the
form
> name
then the PostScript files "name_ss.ps" and "name_dp.ps" are
produced for the structure and dot plot, respectively. Otherwise
the filenames default to rna.ps and dot.ps. Existing files of the
same name will be overwritten.
The program will continue to read new sequences until a line
consisting of the single character @ or an end of file condition is
encountered.
OPTIONS
- -p
- Calculate the partition function and base pairing probability
matrix in addition to the mfe structure. Default is calculation of
mfe structure only. Prints a coarse representation of the pair
probabilities in form of a pseudo bracket notation, the ensemble
free energy, the frequency of the mfe structure, and the structural
diversity. See the description of pf_fold() and mean_bp_dist() in
the RNAlib documentation for details.
Note that unless you also specify -d2 or -d0, the partition function and mfe calculations will use a slightly different energy model. See the discussion of dangling end options below. - -p0
- Calculate the partition function but not the pair probabilities, saving about 50% in runtime. Prints the ensemble free energy -kT ln(Z).
- -C
- Calculate structures subject to constraints. The program reads first the sequence, then a string containing constraints on the structure encoded with the symbols: | (the corresponding base has to be paired x (the base is unpaired) < (base i is paired with a base j>i) > (base i is paired with a base j<i) and matching brackets ( ) (base i pairs base j) With the exception of "|", constraints will disallow all pairs conflicting with the constraint. This is usually sufficient to enforce the constraint, but occasionally a base may stay unpaired in spite of constraints. PF folding ignores constraints of type "|".
- -T temp
- Rescale energy parameters to a temperature of temp C. Default is 37C.
- -4
- Do not include special stabilizing energies for certain tetra-loops. Mostly for testing.
- -d[0|1|2|3]
- How to treat "dangling end" energies for bases adjacent to
helices in free ends and multi-loops: With (-d1) only unpaired
bases can participate in at most one dangling end, this is the
default for mfe folding but unsupported for the partition function
folding. With -d2 this check is ignored, dangling energies
will be added for the bases adjacent to a helix on both sides in
any case; this is the default for partition function folding (-p).
-d or -d0 ignores dangling ends altogether (mostly
for debugging).
With -d3 mfe folding will allow coaxial stacking of adjacent helices in multi-loops. At the moment the implementation will not allow coaxial stacking of the two interior pairs in a loop of degree 3 and works only for mfe folding.
Note that by default (as well as with -d1 and -d3) pf and mfe folding treat dangling ends differently. Use -d2 in addition to -p to ensure that both algorithms use the same energy model. - -noLP
- Produce structures without lonely pairs (helices of length 1). For partition function folding this only disallows pairs that can only occur isolated. Other pairs may still occasionally occur as helices of length 1.
- -noGU
- Do not allow GU pairs.
- -noCloseGU
- Do not allow GU pairs at the end of helices.
- -e 1|2
- Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.
- -P <paramfile>
- Read energy parameters from paramfile, instead of using the default parameter set. A sample parameter file should accompany your distribution. See the RNAlib documentation for details on the file format.
- -nsp pairs
- Allow other pairs in addition to the usual AU,GC,and GU pairs. pairs is a comma separated list of additionally allowed pairs. If a the first character is a "-" then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy.
- -S scale
- In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences. You can also recompile the program to use double precision (see the README file).
- -circ
- Assume a circular (instead of linear) RNA molecule. Currently works only for mfe folding.
REFERENCES
The calculation of mfe structures is based on dynamic programming algorithm originally developed by M. Zuker and P. Stiegler. The partition function algorithm is based on work by J.S. McCaskill. 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
A. Walter, D Turner, J Kim, M Lyttle, P M[:u]ller, D Mathews, M Zuker "Coaxial stacking of helices enhances binding of oligoribonucleotides.." PNAS, 91, pp 9218-9222, 1994
If you use this program in your work you might want to cite:
I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M.
Tacker, P. Schuster (1994) Fast Folding and Comparison of RNA
Secondary Structures. Monatshefte f. Chemie 125: 167-188
M. Zuker, P. Stiegler (1981) Optimal computer folding of large RNA
sequences using thermodynamic and auxiliary information, Nucl Acid
Res 9: 133-148
J.S. McCaskill (1990) The equilibrium partition function and base
pair binding probabilities for RNA secondary structures,
Biopolymers 29: 1105-1119
D. Adams (1979) The hitchhiker's guide to the galaxy, Pan Books,
London