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 right half,
and one square for each pair in the minimum free energy structure
in the lower left 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.

Sequences are read in a simple text format where each sequence
occupies a single line. Each sequence may be preceded by a line of
the form

> name

to assign a name to the sequence. If a name is given in the
input

PostScript files "name_ss.ps" and "name_dp.ps" are produced for
the structure and dot plot, respectively. Otherwise the file names
default to rna.ps and dot.ps. Existing files of the same name will
be overwritten.

The input format is similar to fasta except that even long
sequences may not be interrupted by line breaks, and the header
lines are optional. The program will continue to read new sequences
until a line consisting of the single character @ or an end of file
condition is encountered.

**-p**- Calculate the partition function and base pairing probability
matrix in addition to the mfe structure. Default is calculation of
mfe structure only. In addition to the MFE structure we print a
coarse representation of the pair probabilities in form of a pseudo
bracket notation, followed by the ensemble free energy, as well as
the centroid structure derived from the pair probabilities together
with its free energy and distance to the ensemble. Finally it
prints the frequency of the mfe structure, and the structural
diversity (mean distance between the structures in the ensemble).
See the description of pf_fold() and mean_bp_dist() and centroid()
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).
**-p2**- In addition to pair probabilities compute stack probabilities, i.e. the probability that a pair (i,j) and the immediately interior pair (i+1,j-1) are formed simultaneously. A second postscript dot plot called "name_dp2.ps", or "dot2.ps" (if the sequence does not have a name), is produced that contains pair probabilities in the upper right half and stack probabilities in the lower left.
**-MEA***[gamma]*- Calculate an MEA (maximum expected accuracy) structure, where the expected accuracy is computed from the pair probabilities: each base pair (i,j) gets a score 2*gamma*p_ij and the score of an unpaired base is given by the probability of not forming a pair. The parameter gamma tunes the importance of correctly predicted pairs versus unpaired bases. Thus, for small values of gamma the MEA structure will contain only pairs with very high probability. The default value is gamma=1. Using -MEA implies -p for computing the pair probabilities.
**-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. **-circ**- Assume a circular (instead of linear) RNA molecule.
**-noPS**- Do not produce postscript drawing of the mfe structure.

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

I.L. Hofacker & P.F. Stadler (2006) Memory Efficient Folding
Algorithms for Circular RNA Secondary Structures,
Bioinformatics

A.F. BompfÃ¼newerer, R. Backofen, S.H. Bernhart, J.
Hertel, I.L. Hofacker, P.F. Stadler, S. Will (2007) "Variations on
RNA Folding and Alignment: Lessons from Benasque" J. Math.
Biol.

D. Adams (1979) The hitchhiker's guide to the galaxy, Pan Books,
London

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Time: 07:19:16 GMT, February 23, 2011