NAME

       RNA2Dfold - manual page for RNA2Dfold 2.6.4

SYNOPSIS

       RNA2Dfold [OPTION]...

DESCRIPTION

       RNA2Dfold 2.6.4

       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

       --full-help
              Print help, including hidden options, and exit

       -V, --version
              Print version and exit

   I/O Options:
              Command line options for input and output (pre-)processing

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

       --noconv
              Do not automatically substitute nucleotide "T" with "U".

              (default=off)

   Algorithms:
              Select additional algorithms which should be included  in  the  calculations.   The  Minimum  free
              energy (MFE) and a structure representative are calculated in any case.

       -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>,...)

       -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

       -S, --pfScale=DOUBLE
              In the calculation of the pf use scale*mfe as an estimate for the ensemble free  energy  (used  to
              avoid overflows).

              (default=`1.07')

              The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences.

       --noBT do not backtrack structures, calculate energy contributions only

              (default=off)

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

              (default=off)

   Energy Parameters:
              Energy parameter sets can be adapted or loaded from user-provided input files

       -T, --temp=DOUBLE
              Rescale energy parameters to a temperature of temp C. Default is 37C.

              (default=`37.0')

       -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. The placeholder file name 'DNA' can  be  used
              to load DNA parameters without the need to actually specify any input file.

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

              (default=off)

              Mostly for testing.

       --salt=DOUBLE
              Set salt concentration in molar (M). Default is 1.021M.

   Model Details:
              Tweak the energy model and pairing rules additionally using the following parameters

       -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)

       --helical-rise=FLOAT
              Set the helical rise of the helix in units of Angstrom.

              (default=`2.8')

              Use with caution! This value will be re-set automatically to 3.4 in case DNA parameters are loaded
              via -P DNA and no further value is provided.

       --backbone-length=FLOAT
              Set the average backbone length for looped regions in units of Angstrom.

              (default=`6.0')

              Use with caution! This value will be re-set automatically to  6.76  in  case  DNA  parameters  are
              loaded via -P DNA and no further value is provided.

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 2.6.4                                   January 2025                                      RNA2DFOLD(1)