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       RNApaln - manual	page for RNApaln 2.4.14

       RNApaln [OPTIONS]...

       RNApaln 2.4.14

       RNA alignment based on sequence base pairing propensities

       Uses  string-alignment  techniques  to perform fast pairwise structural
       alignments of RNAs. Similar to RNApdist secondary structure is incorpo-
       rated  in  an  approximate manner by computing base pair	probabilities,
       which are then reduced to a vector holding the probability that a  base
       is paired upstream, downstream, or remains unpaired. Such pair propsen-
       sity vectors can	then be	compared using standard	alignment  algorithms.
       In  contrast  to	RNApdist, RNApaln performs similarity (instead of dis-
       tance) alignments, considers both sequence and  structure  information,
       and  uses  affine  (rather  than	linear)	gap costs. RNApaln can perform
       semi-local alignments by	using free end gaps, a	true  local  alignment
       mode is planned.

       The same	approach has since been	used in	the StraL program from Gerhard
       Steeger's group.	Since StraL has	optimized parameters  and  a  multiple
       alignment mode, it be be	currently the better option.

       -h, --help
	      Print help and exit

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

	      Print help, including hidden options, and	exit

       -V, --version
	      Print version and	exit

   General Options:
	      Below  are command line options which alter the general behavior
	      of this program

       -B, --printAlignment[=filename]
	      Print an "alignment" with	gaps of	the

	      The aligned structures are written  to  filename,	 if  specified
	      Otherwise	 output	is written to stdout, unless the -Xm option is
	      set in which case	"backtrack.file" is used.


	      The following symbols are	used:

       (      )	 essentially upstream (downstream) paired bases

       {      }	 weakly	upstream (downstream) paired bases

       |      strongly paired bases without preference

       ,      weakly paired bases without preference

       .      essentially unpaired bases.

	      Do not automatically substitude nucleotide "T" with "U"


	      Select additional	algorithms which should	 be  included  in  the

       -X, --mode=pmfc
	      Set the alignment	mode to	be used

	      The  alignment  mode  is passed as a single character value. The
	      following	options	are available: 'p' -  Compare  the  structures
	      pairwise,	 that  is  first with 2nd, third with 4th etc. This is
	      the default.

       'm'    -	Calculate the distance matrix between all structures. The out-
	      put is

	      formatted	as a lower triangle matrix.

	      'f' - Compare each structure to the first	one.

	      'c' - Compare continuously, that is i-th with (i+1)th structure.

   Model Details:
	      Set the gap open penalty

	      Set the gap extension penalty

	      Set  the weight of sequence (compared to structure) in the scor-
	      ing function.

	      Use free end-gaps


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

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


       -d, --dangles=INT
	      How to treat "dangling end" energies for bases adjacent  to  he-
	      lices in free ends and multi-loops


	      With -d1 only unpaired bases can participate in at most one dan-
	      gling end.  With -d2 this	check is  ignored,  dangling  energies
	      will be added for	the bases adjacent to a	helix on both sides in
	      any case;	this is	the default for	 mfe  and  partition  function
	      folding  (-p).   The option -d0 ignores dangling ends altogether
	      (mostly for debugging).  With -d3	mfe folding will allow coaxial
	      stacking	of  adjacent helices in	multi-loops. At	the moment the
	      implementation will not allow coaxial stacking of	the two	 inte-
	      rior pairs in a loop of degree 3 and works only for mfe folding.

	      Note that	with -d1 and -d3 only the MFE computations will	be us-
	      ing this setting while partition function	uses -d2 setting, i.e.
	      dangling ends will be treated differently.

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


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

       --noGU Do not allow GU pairs


	      Do not allow GU pairs at the end of helices


       -P, --paramFile=paramfile
	      Read  energy parameters from paramfile, instead of using the de-
	      fault parameter set.

	      Different	sets of	energy parameters for RNA and DNA  should  ac-
	      company your distribution.  See the RNAlib documentation for de-
	      tails on the file	format.	When passing the placeholder file name
	      "DNA",  DNA  parameters  are loaded without the need to actually
	      specify any input	file.

	      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.

       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

       Bonhoeffer S, McCaskill J S, Stadler  P	F,  Schuster  P	 (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  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

       Peter F Stadler,	Ivo L Hofacker,	Sebastian Bonhoeffer

       If in doubt our program is right, nature	is at fault.  Comments	should
       be sent to

RNApaln	2.4.14			  August 2019			    RNAPALN(1)


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