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.