Provided by: vienna-rna_2.5.1+dfsg-1_amd64 bug

NAME

       RNAplot - manual page for RNAplot 2.5.1

SYNOPSIS

       RNAplot [OPTIONS] [<input0>] [<input1>]...

DESCRIPTION

       RNAplot 2.5.1

       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  radial  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 sequence 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 explicitly  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 using multiple
              threads.  (default=`0')

              Default processing of input data  is  performed  in  a  serial  fashion,  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  consumption  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 parameter 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 structure. 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 nucleotides with
              frequency greater than average in IUPAC notation.

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

       --aln  Produce a colored and structure annotated alignment in  PostScript  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 plotting layout algorithm.  (default=`1')

              Select  the  layout algorithm that computes the nucleotide coordinates.  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.  (default=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 following 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 parameter, the first number can be specified to
              the users requirements. Note: negative numbers are not allowed.  Note: Setting this
              parameter implies to ignore  any  IDs  retrieved  from  the  input  data,  i.e.  it
              activates the --auto-id flag.

       --filename-delim=STRING
              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 characters.  Note,  that  the  default  delimiter
              ALWAYS  is  the  first  character  of  the  "ID  delimiter" as supplied through the
              --id-delim option. If the delimiter is a whitespace  character  or  empty,  invalid
              characters will be simply removed rather than substituted. Currently, we regard the
              following characters as illegal for use in filenames:  backslash  '\',  slash  '/',
              question  mark  '?',  percent  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 structure 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 character or simply removed, (see
              also the parameter option --filename-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 Structures", 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  modification  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.