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.