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RNADISTANCE(1)			 User Commands			RNADISTANCE(1)

NAME
       RNAdistance - manual page for RNAdistance 2.4.14

SYNOPSIS
       RNAdistance [OPTIONS]...

DESCRIPTION
       RNAdistance 2.4.14

       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	brack-
       ets  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,  respec-
       tively.	 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 consist-
       ing of the single character @ or	an end of file	condition  is  encoun-
       tered.  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	align-
	      ment otherwise tree editing is used.  Any	 combination  of  dis-
	      tances can bespecified.

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

	      Possible	arguments  for this option are:	-Xp compare the	struc-
	      tures 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	struc-
	      tures.

	      (default=off)

       -B, --backtrack[=<filename>]
	      Print an "alignment" with	gaps of	the structures,	to show	match-
	      ing substructures.  The aligned structures are written to	<file-
	      name>, 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	Struc-
       tures", 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	struc-
       tures 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  modifica-
       tion 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 2.4.14		  August 2019			RNADISTANCE(1)

NAME | SYNOPSIS | DESCRIPTION | REFERENCES | AUTHOR | REPORTING BUGS

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