NAME

       RNApdist - manual page for RNApdist 2.5.1

SYNOPSIS

       RNApdist [OPTION]...

DESCRIPTION

       RNApdist 2.5.1

       Calculate distances between thermodynamic RNA secondary structures ensembles

       This program reads RNA sequences from stdin and calculates structure distances between the
       thermodynamic ensembles of their secondary structures.

       To do this the partition function and matrix of base pairing probabilities is computed for
       each  sequence.  The  probability  matrix is then condensed into a vector holding for each
       base  the  probabilities  of  being  unpaired,  paired  upstream,  or  paired  downstream,
       respectively. These profiles are compared by a standard alignment algorithm.

       The  base  pair  probabilities are also saved as postscript "dot plots" (as in RNAfold) in
       the files  "name_dp.ps", where name is the name of the sequence, or a number if unnamed.

       -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

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

              (default=off)

   Algorithms:
       -X, --compare=p|m|f|c
              Specify the comparison directive.  (default=`p')

              Possible arguments for this option are: -Xp compare the  structures  pairwise  (p),
              i.e. first with 2nd, third with 4th etc.  -Xm calculate the distance matrix between
              all structures. The output is formatted as a lower triangle  matrix.   -Xf  compare
              each  structure  to  the  first  one.   -Xc compare continuously, that is i-th with
              (i+1)th structure.

       -B, --backtrack[=<filename>]
              Print an "alignment" with gaps of the profiles. The aligned structures are  written
              to <filename>, if specified.

              (default=`none')

              Within the profile output, the following symbols will be used:

       ()     essentially upstream (downstream) paired bases

       {}     weakly upstream (downstream) paired bases

       |      strongly paired bases without preference

       ,      weakly paired bases without preference

       .      essentially unpaired bases.

              If <filename> is not specified, the output is written to stdout, unless the

              "-Xm" option is set in which case "backtrack.file" is used.

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

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

              (default=off)

       -d, --dangles=INT
              set energy model for treatment of dangling bases

              (possible values="0", "2" default=`2')

       --noLP Produce structures without lonely pairs (helices of length 1).

              (default=off)

              For partition function folding this  only  disallows  pairs  that  can  only  occur
              isolated. Other pairs may still occasionally occur as helices of length 1.

       --noGU Do not allow GU pairs

              (default=off)

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

              (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 any input file.

       --nsp=STRING
              Allow other pairs in addition to the usual AU,GC,and GU pairs.

              Its argument is a comma separated list of additionally allowed pairs. If the  first
              character  is  a  "-"  then  AB  will imply that AB and BA are allowed pairs.  e.g.
              RNAfold -nsp -GA  will allow GA  and  AG  pairs.  Nonstandard  pairs  are  given  0
              stacking energy.

       -e, --energyModel=INT
              Rarely  used option to fold sequences from the artificial ABCD... alphabet, where A
              pairs B, C-D etc.  Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.

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

       S. Bonhoeffer, J.S. McCaskill, P.F. Stadler,  P.  Schuster  (1993),  "RNA  multi-structure
       landscapes", Euro Biophys J:22, pp 13-24

       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

       Peter F Stadler, Ivo L Hofacker, Sebastian Bonhoeffer.

REPORTING BUGS

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