NAME

       RNApdist - manual page for RNApdist 2.4.17

SYNOPSIS

       RNApdist [OPTION]...

DESCRIPTION

       RNApdist 2.4.17

       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.

RNApdist 2.4.17                                   January 2022                                       RNAPDIST(1)