NAME

SYNOPSIS

DESCRIPTION

predicts RNA secondary structures including pseudoknots

Computes RNA secondary structures by first making two sequence intervals accessible and unpaired using the algorithm of RNAplfold and then calculating the energy of the interaction of those two intervals. The algorithm uses O(n^2*w^4) CPU time and O(n*w^2) memory space. The algorithm furthermore always considers dangle=2 model.

It also produces a PostScript file with a plot of the pseudoknot-free secondary structure graph, in which the bases forming the pseuodknot are marked red.

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

-h, --help

Print help and exit

--detailed-help

Print help, including all details and hidden options, and exit

-V, --version

Print version and exit

-c, --cutoff=FLOAT

Report only base pairs with an average probability > cutoff in the dot plot

(default=`0.01')

-T, --temp=DOUBLE

Rescale energy parameters to a temperature of temp C. Default is 37C.

-4, --noTetra

Do not include special stabilizing energies for certain tetra-loops. Mostly for testing.

(default=off)

--noLP

Produce structures without lonely pairs (helices of length 1).

(default=off)

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

(default=off)

--noClosingGU

Do not allow GU pairs at the end of helices

(default=off)

--noconv

Do not automatically substitude nucleotide "T" with "U"

(default=off)

--nsp=STRING

Allow other pairs in addition to the usual AU,GC,and GU pairs.

(default=`empty')

Its argument is a comma separated list of additionally allowed pairs. If 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.

-e, --energyCutoff=DOUBLE

Energy cutoff or pseudoknot initiation cost. Minimum energy gain of a pseudoknot interaction for it to be returned. Pseudoknots with smaller energy gains are rejected.

(default=`-8.10')

-P, --paramFile=paramfile

Read energy parameters from paramfile, instead of using the default parameter set.

Different sets of energy parameters for RNA and DNA should accompany your distribution. See the RNAlib documentation for details on the file format. When passing the placeholder file name "DNA", DNA parameters are loaded without the need to actually specify any input file.

-v, --verbose

print verbose output

(default=off)

-s, --subopts=DOUBLE

print suboptimal structures whose energy difference of the pseudoknot to the optimum pseudoknot is smaller than the given value.

(default=`0.0')

NOTE: The final energy of a structure is calculated as the sum of the pseudoknot interaction energy, the penalty for initiating a pseudoknot and the energy of the pseudoknot-free part of the structure. The -s option only takes the pseudoknot interaction energy into account, so the final energy differences may be bigger than the specified value (default=0.).

REFERENCES

R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011), "ViennaRNA Package 2.0", Algorithms for Molecular Biology: 6:26

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, pp 167-188

R. Lorenz, I.L. Hofacker, P.F. Stadler (2016), "RNA folding with hard and soft constraints", Algorithms for Molecular Biology 11:1 pp 1-13

The energy parameters are taken from:

D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M. Zuker, D.H. Turner (2004), "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure", Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292

D.H Turner, D.H. Mathews (2009), "NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure", Nucleic Acids Research: 38, pp 280-282

AUTHOR

REPORTING BUGS