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RNAPALN(1)			 User Commands			    RNAPALN(1)

NAME
       RNApaln - manual	page for RNApaln 2.4.14

SYNOPSIS
       RNApaln [OPTIONS]...

DESCRIPTION
       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

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

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

       profiles
	      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.

	      (default=`stdout')

	      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.

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

	      (default=off)

   Algorithms:
	      Select additional	algorithms which should	 be  included  in  the
	      calculations.

       -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:
       --gapo=open
	      Set the gap open penalty

       --gape=ext
	      Set the gap extension penalty

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

       --endgaps
	      Use free end-gaps

	      (default=off)

       -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
	      How to treat "dangling end" energies for bases adjacent  to  he-
	      lices in free ends and multi-loops

	      (default=`2')

	      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).

	      (default=off)

	      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

	      (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 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.

       --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	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

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.

RNApaln	2.4.14			  August 2019			    RNAPALN(1)

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

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