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