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RNAPLOT(1)			 User Commands			    RNAPLOT(1)

NAME
       RNAplot - manual	page for RNAplot 2.4.14

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

DESCRIPTION
       RNAplot 2.4.14

       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. A value of 0 indicates to use as many par-
	      allel threads as computation cores are available.

	      (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.

       -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:
	      For each column of the alignment output the set  of  nucleotides
	      with frequency greater than average in IUPAC notation.

	      (default=off)

       --covar
	      Annotate covariance of base pairs	in consensus structure

	      (default=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.

	      (default=`60')

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

       -t, --layout-type=INT
	      Choose the 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. Available formats are:

       PostScript (ps),	Graph Meta Language (gml),
	      Scalable Vector Graphics (svg), and XRNA save file (xrna).  Out-
	      put  filenames  will  end	 in ".ps" ".gml" ".svg"	".ss", respec-
	      tively.

	      (default=`ps')

       --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=delimiter
	      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=delimiter
	      Change the delimiting character that is used

	      for sanitized filenames

	      (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	2.4.14			  August 2019			    RNAPLOT(1)

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

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