NAME

       RNAdistance - manual page for RNAdistance 2.5.1

SYNOPSIS

       RNAdistance [OPTION]...

DESCRIPTION

       RNAdistance 2.5.1

       Calculate distances between RNA secondary structures

       This program reads RNA secondary structures from stdin and calculates one or more measures
       for their dissimilarity, based on tree or  string  editing  (alignment).  In  addition  it
       calculates  a  "base  pair  distance"  given  by  the  number of base pairs present in one
       structure, but not the other. For structures of different length base pair distance is not
       recommended.

       RNAdistance  accepts  structures in bracket format, where matching brackets symbolize base
       pairs and unpaired bases are represented by a dot ".", or coarse  grained  representations
       where  hairpins,  interior  loops,  bulges,  multiloops,  stacks  and  external  bases are
       represented by (H), (I), (B), (M), (S), and (E), respectively.  These  can  be  optionally
       weighted. Full structures can be represented in the same fashion using the identifiers (U)
       and (P) for unpaired and paired bases, respectively.  We call this the HIT  representation
       (you don't want to know what this means).  For example the following structure consists of
       2 hairpins joined by a multiloop:

         .((..(((...)))..((..)))).       full structure (usual format);
         (U)((U2)((U3)P3)(U2)((U2)P2)P2) HIT structure;
         ((H)(H)M)  or
         ((((H)S)((H)S)M)S)              coarse grained structure;
         (((((H3)S3)((H2)S2)M4)S2)E2)    weighted coarse grained.

       The program will continue to read new structures until a line  consisting  of  the  single
       character  @  or an end of file condition is encountered. Input lines neither containing a
       valid structure nor starting with > are ignored.

       -h, --help
              Print help and exit

       --detailed-help
              Print help, including all details and hidden options, and exit

       -V, --version
              Print version and exit

       -D, --distance=fhwcFHWCP
              Specify the distance representation to be used in calculations.

              (default=`f')

              Use the full, HIT, weighted coarse,  or  coarse  representation  to  calculate  the
              distance. Capital letters indicate string alignment otherwise tree editing is used.
              Any combination of distances can bespecified.

       -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.

       -S, --shapiro
              Use the Bruce Shapiro's cost matrix for comparing coarse structures.

              (default=off)

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

              (default=`none')

              If  <filename>  is  not  specified, the output is written to stdout, unless the -Xm
              option is set in which case "backtrack.file" is used.

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

       B.A. Shapiro (1988), "An  algorithm  for  comparing  multiple  RNA  secondary  structures"
       CABIOS: 4, pp 381-393

       B.A.  Shapiro,  K.  Zhang  (1990), "Comparing multiple RNA secondary structures using tree
       comparison", CABIOS: 6, pp 309-318

       W. Fontana, D.A.M. Konings, P.F. Stadler and P. Schuster  P  (1993),  "Statistics  of  RNA
       secondary structures", Biopolymers: 33, pp 1389-1404

       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

       Walter Fontana, Ivo L Hofacker, Peter F Stadler

REPORTING BUGS

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