NAME

       RNA2Dfold - manual page for RNA2Dfold 2.5.1

SYNOPSIS

       RNA2Dfold [OPTION]...

DESCRIPTION

       RNA2Dfold 2.5.1

       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.

RNA2Dfold 2.5.1                                    April 2024                                       RNA2DFOLD(1)