RNAfold - Manual

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RNAfold - Manual (generated by man2html)

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]

DESCRIPTION

RNAfold reads RNA sequences from stdin and calculates their minimum free energy (mfe) structure, partition function (pf) and base pairing probability matrix. 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 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.
-p0: Calculate the pf without pairing matrix and print the ensemble free energy -kT ln(Z). This is much faster.
-C: Calculate structures subject to constraints. The programm reads first the sequence then the a string containg 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 tetraloops. Mostly for tesing.
-d[0|1|2|3]: How to treat "dangling end" energies for bases adjacent to helices in free ends and multiloops: Normally (-d1) only unpaired bases can participate in at most one dangling end. With -d2 this check is ignored, this is the default for partition function folding (-p). -d or FB-d0 ignores dangling ends altogether. Note that by default pf and mfe folding treat dangling ends differently, use -d2 in addition to -p to ensure that both algorithms use the same energy model.
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. PF folding will work as with -d2.
-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 parameterfile 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 seperated 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, usefull values are 1.0 to 1.2. Occasionally needed for long sequences. You can also recompile the programm to use double precision (see the README file).