RNAplot — ViennaRNA Package

# RNAplot

RNAplot - manual page for RNAplot 2.7.2

## Synopsis

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

## DESCRIPTION

RNAplot 2.7.2

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

-v, --verbose

  Be verbose. (default=off)

  Lower the log level setting such that even INFO messages are passed through.

### I/O Options:

> Command line options for input and output (pre-)processing

-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.

-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.

-f, --output-format=format

  Specify output file format. (possible values=”eps”, “svg”, “gml”, “xrna”, “ssv” default=”eps”)

  Available formats are: Encapsulated PostScript (`eps`), Scalable Vector Graphics (`svg`), Graph Meta Language (`gml`), and XRNA save file (`xrna`). Output filenames will end in “.eps” “.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=STRING

  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=CHAR

  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 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=CHAR

  Change the delimiting character used in 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`).

--log-level=level

  Set log level threshold. (default=”2”)

  By default, any log messages are filtered such that only warnings (level 2) or errors (level 3) are printed. This setting allows for specifying the log level threshold, where higher values result in fewer information. Log-level 5 turns off all messages, even errors and other critical information.

--log-file[=filename]

  Print log messages to a file instead of stderr. (default=”RNAplot.log”)

--log-time

  Include time stamp in log messages.

  (default=off)

--log-call

  Include file and line of log calling function.

  (default=off)

### Plotting:

> Command line options for changing the default behavior of structure layout and pairing probability plots

--covar

  Annotate covariance of base pairs in consensus structure.

  (default=off)

--covar-threshold=FLOAT

  Set the threshold of maximum counter examples for coloring consensus structure plot.

  (default=”2”)

  Floating point numbers between 0 and 1 are treated as frequencies among all sequencesin the alignment. All other will be truncated to integer and used as absolute number of counter examples.

--covar-min-sat=FLOAT

  Set the minimum saturation for coloring consensus structure plot.

  (default=”0.2”)

  Floating point number >= 0 and smaller than 1.

--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. (possible values=”0”, “1”, “2”, “3”, “4” 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)

## 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.