NAME

       RNAdistance - manual page for RNAdistance 2.6.4

SYNOPSIS

       RNAdistance [OPTION]...

DESCRIPTION

       RNAdistance 2.6.4

       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.

RNAdistance 2.6.4                                 January 2025                                    RNADISTANCE(1)