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RNAPLOT(1)			 User Commands			    RNAPLOT(1)

NAME
       RNAplot - manual	page for RNAplot 2.4.18

SYNOPSIS
       RNAplot [OPTIONS] [_input0_] [_input1_]...

DESCRIPTION
       RNAplot 2.4.18

       Draw RNA	Secondary Structures

       The  program reads (aligned) RNA	sequences and structures in the	format
       as produced by RNAfold or Stockholm 1.0 and produces  drawings  of  the
       secondary  structure  graph.   Coordinates for the structure graphs are
       produced	using either E.	Bruccoleri's naview routines, or a simple  ra-
       dial  layout  method.   For  aligned sequences and consensus structures
       (--msa option) the graph	may be annotated  by  covariance  information.
       Additionally,  a	 color-annotated EPS alignment figure can be produced,
       similar to that obtained	by RNAalifold and  RNALalifold.	  If  the  se-
       quence  was  preceded  by  a  FASTA header, or if the multiple sequence
       alignment contains an ID	field, these IDs will be taken	as  names  for
       the  output file(s): "name_ss.ps" and "name_aln.ps". Otherwise "rna.ps"
       and "aln.ps" will be used. This behavior	may be over-ruled  by  explic-
       itly  setting  a	 filename prefix using the --auto-id option.  Existing
       files of	the same name will be overwritten.

       -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

       -j, --jobs[=number]
	      Split batch input	into jobs and start processing in parallel us-
	      ing multiple threads.  (default=`0')

	      Default  processing of input data	is performed in	a serial fash-
	      ion, i.e.	one sequence at	a time.	Using this switch, a user  can
	      instead start the	computation for	many sequences in the input in
	      parallel.	RNAplot	will create as many parallel computation slots
	      as specified and assigns input sequences of the input file(s) to
	      the available slots. Note, that this increases  memory  consump-
	      tion  since  input alignments have to be kept in memory until an
	      empty compute slot is available and each	running	 job  requires
	      its  own dynamic programming matrices. A value of	0 indicates to
	      use as many parallel threads as computation cores	are available.

       -i, --infile=<filename>
	      Read a file instead of reading from stdin.

	      The default behavior of RNAplot is to read input from  stdin  or
	      the  file(s)  that follow(s) the RNAplot command.	Using this pa-
	      rameter the user can specify input file names where data is read
	      from.  Note,  that  any additional files supplied	to RNAplot are
	      still processed as well.

       -a, --msa
	      Input is multiple	sequence alignment in  Stockholm  1.0  format.
	      (default=off)

	      Using  this flag indicates that the input	is a multiple sequence
	      alignment	(MSA) instead of (a) single  sequence(s).  Note,  that
	      only  STOCKHOLM  format allows one to specify a consensus	struc-
	      ture. Therefore, this is the only	supported MSA format for now!

       --mis  Output "most informative sequence" instead of  simple  consensus
	      (default=off)

	      For  each	 column	of the alignment output	this is	the set	of nu-
	      cleotides	with frequency greater than average in IUPAC notation.

       --covar
	      Annotate covariance of base pairs	in consensus structure.	  (de-
	      fault=off)

       --aln  Produce  a  colored  and	structure annotated alignment in Post-
	      Script format in the file	"aln.ps"  in  the  current  directory.
	      (default=off)

       --aln-EPS-cols=INT
	      Number  of  columns  in  colored	EPS  alignment	output.	  (de-
	      fault=`60')

	      A	value less than	1 indicates that  the  output  should  not  be
	      wrapped at all.

       -t, --layout-type=INT
	      Choose the plotting layout algorithm.  (default=`1')

	      Select the layout	algorithm that computes	the nucleotide coordi-
	      nates.  Currently, the following algorithms are available:

	      0: simple	radial layout

	      1: Naview	layout (Bruccoleri et al. 1988)

	      2: circular layout

	      3: RNAturtle (Wiegreffe et al. 2018)

	      4: RNApuzzler (Wiegreffe et al. 2018)

       --noOptimization
	      Disable the drawing  space  optimization	of  RNApuzzler.	  (de-
	      fault=off)

       --ignoreExteriorIntersections
	      Ignore intersections with	the exterior loop

       within the RNA-tree.
	      (default=off)

       --ignoreAncestorIntersections
	      Ignore ancestor intersections within the

       RNA-tree.
	      (default=off)

       --ignoreSiblingIntersections
	      Ignore sibling intersections within the

       RNA-tree
	      (default=off)

       --allowFlipping
	      Allow  flipping  of  exterior  loop branches to resolve exterior
	      branch intersections.  (default=off)

       -o, --output-format=ps|gml|xrna|svg
	      Specify output format.  (default=`ps')

	      Available	formats	are:  PostScript  (ps),	 Graph	Meta  Language
	      (gml),  Scalable	Vector	Graphics  (svg),  and  XRNA  save file
	      (xrna). Output filenames will end	in ".ps" ".gml"	".svg"	".ss",
	      respectively.

       --pre=string
	      Add annotation macros to postscript file,	and add	the postscript
	      code in "string" just before the code  to	 draw  the  structure.
	      This is an easy way to add annotation.

       --post=string
	      Same  as	--pre but in contrast to adding	the annotation macros.
	      E.g to mark position 15 with circle use --post "15 cmark".

       --auto-id
	      Automatically generate an	ID for each sequence.  (default=off)

	      The default mode of RNAfold is to	automatically determine	an  ID
	      from  the	input sequence data if the input file format allows to
	      do that. Sequence	IDs are	usually	given in the FASTA  header  of
	      input sequences. If this flag is active, RNAfold ignores any IDs
	      retrieved	from the input and automatically generates an  ID  for
	      each  sequence.  This  ID	consists of a prefix and an increasing
	      number. This flag	can also be used to add	a FASTA	header to  the
	      output even if the input has none.

       --id-prefix=prefix
	      Prefix  for  automatically generated IDs (as used	in output file
	      names).  (default=`sequence')

	      If this parameter	is set,	each sequence will  be	prefixed  with
	      the  provided string. Hence, the output files will obey the fol-
	      lowing naming scheme: "prefix_xxxx_ss.ps"	 (secondary  structure
	      plot),   "prefix_xxxx_dp.ps"   (dot-plot),  "prefix_xxxx_dp2.ps"
	      (stack probabilities), etc. where	xxxx is	the  sequence  number.
	      Note: Setting this parameter implies --auto-id.

       --id-delim=STRING
	      Change  the  delimiter  between prefix and increasing number for
	      automatically generated IDs (as  used  in	 output	 file  names).
	      (default=`_')

	      This  parameter  can be used to change the default delimiter "_"
	      between

	      the prefix string	and the	increasing  number  for	 automatically
	      generated	ID.

       --id-digits=INT
	      Specify  the  number  of	digits of the counter in automatically
	      generated	alignment IDs.	(default=`4')

	      When alignments IDs are automatically generated, they receive an
	      increasing  number,  starting with 1. This number	will always be
	      left-padded by leading zeros, such that the number  takes	 up  a
	      certain  width. Using this parameter, the	width can be specified
	      to the users need. We allow numbers in the  range	 [1:18].  This
	      option implies --auto-id.

       --id-start=LONG
	      Specify  the  first  number in automatically generated alignment
	      IDs.  (default=`1')

	      When sequence IDs	are automatically generated, they  receive  an
	      increasing  number,  usually starting with 1. Using this parame-
	      ter, the first number can	be specified  to  the  users  require-
	      ments.  Note:  negative  numbers are not allowed.	 Note: Setting
	      this parameter implies to	ignore any IDs retrieved from the  in-
	      put data,	i.e. it	activates the --auto-id	flag.

       --filename-delim=STRING
	      Change the delimiting character that is used for sanitized file-
	      names

	      (default=`ID-delimiter')

	      This parameter can be used to change  the	 delimiting  character
	      used  while sanitizing filenames,	i.e. replacing invalid charac-
	      ters. Note, that the default delimiter ALWAYS is the first char-
	      acter  of	 the "ID delimiter" as supplied	through	the --id-delim
	      option. If the delimiter is a whitespace character or empty, in-
	      valid characters will be simply removed rather than substituted.
	      Currently, we regard the following characters as illegal for use
	      in  filenames: backslash '\', slash '/', question	mark '?', per-
	      cent sign	'%', asterisk '*', colon ':', pipe symbol '|',	double
	      quote '"', triangular brackets '<' and '>'.

       --filename-full
	      Use full FASTA header to create filenames.  (default=off)

	      This parameter can be used to deactivate the default behavior of
	      limiting output filenames	to the first word of the sequence  ID.
	      Consider	the  following	example:  An  input  with FASTA	header
	      ">NM_0001	Homo Sapiens some gene"	usually	produces output	 files
	      with  the	prefix "NM_0001" without the additional	data available
	      in the FASTA header, e.g.	"NM_0001_ss.ps"	for  secondary	struc-
	      ture  plots.  With  this	flag  set, no truncation of the	output
	      filenames	is done, i.e. output filenames receive the full	 FASTA
	      header  data as prefixes.	Note, however, that invalid characters
	      (such as whitespace) will	be substituted by a delimiting charac-
	      ter  or  simply  removed,	(see also the parameter	option --file-
	      name-delim).

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

       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
       Ivo L Hofacker, Ronny Lorenz

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

RNAplot	2.4.18			  April	2021			    RNAPLOT(1)

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

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