NAME

RNA2Dfold - manual page for RNA2Dfold 2.5.0

SYNOPSIS

RNA2Dfold [OPTION]...

DESCRIPTION

RNA2Dfold 2.5.0

Compute MFE structure, partition function and representative sample structures of k,l neighborhoods

The program partitions the secondary structure space into (basepair)distance classes according to two fixed reference structures. It expects a sequence and two secondary structures in dot-bracket notation as its inputs. For each distance class, the MFE representative, Boltzmann probabilities and Gibbs free energy is computed. Additionally, a stochastic backtracking routine allows one to produce samples of representative suboptimal secondary structures from each partition

-h, --help: Print help and exit
--detailed-help: Print help, including all details and hidden options, and exit
-V, --version: Print version and exit

General Options:

: Below are command line options which alter the general behavior of this program

--noconv: Do not automatically substitude nucleotide "T" with "U"

: (default=off)

-j, --numThreads=INT: Set the number of threads used for calculations (only available when compiled with OpenMP support)

Algorithms:

-p, --partfunc: calculate partition function and thus, Boltzmann probabilities and Gibbs free energy

: (default=off)

--stochBT=INT: backtrack a certain number of Boltzmann samples from the appropriate k,l neighborhood(s)
--neighborhood=<k>:<l>: backtrack structures from certain k,l-neighborhood only, can be specified multiple times (<k>:<l>,<m>:<n>,...)
-S, --pfScale=DOUBLE: scaling factor for pf to avoid overflows
--noBT: do not backtrack structures, calculate energy contributions only

: (default=off)

-c, --circ: Assume a circular (instead of linear) RNA molecule.

: (default=off)

Model Details:

-T, --temp=DOUBLE: Rescale energy parameters to a temperature of temp C. Default is 37C.
-K, --maxDist1=INT: maximum distance to first reference structure

: If this value is set all structures that exhibit a basepair distance greater than maxDist1 will be thrown into a distance class denoted by K=L=-1

-L, --maxDist2=INT: maximum distance to second reference structure

: If this value is set all structures that exhibit a basepair distance greater than maxDist1 will be thrown into a distance class denoted by K=L=-1

-4, --noTetra: Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.

: (default=off)

-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 an input file.

-d, --dangles=INT: How to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops

: (possible values="0", "2" default=`2')
: With -d2 dangling energies will be added for the bases adjacent to a helix on both sides
: in any case.
: The option -d0 ignores dangling ends altogether (mostly for debugging).

--noGU: Do not allow GU pairs

: (default=off)

--noClosingGU: Do not allow GU pairs at the end of helices

: (default=off)

REFERENCES

If you use this program in your work you might want to cite:

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

R. Lorenz, C. Flamm, I.L. Hofacker (2009), "2D Projections of RNA folding Landscapes", GI, Lecture Notes in Informatics, German Conference on Bioinformatics 2009: 157, pp 11-20

M. Zuker, P. Stiegler (1981), "Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information", Nucl Acid Res: 9, pp 133-148

J.S. McCaskill (1990), "The equilibrium partition function and base pair binding probabilities for RNA secondary structures", Biopolymers: 29, pp 1105-1119

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

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

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, 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

Ronny Lorenz

REPORTING BUGS

If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at.