                                  vrnaplot



Wiki

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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Plot vrnafold output

Description

   This is a port of the Vienna RNA package program RNAplot.

Algorithm

   See the original documentation for the Vienna RNA package
   http://www.tbi.univie.ac.at/~ivo/RNA/

Usage

   Here is a sample session with vrnaplot


% vrnaplot
Plot vrnafold output
Vienna RNAfold output file: ../vrnafold-keep/rna1.vrnafold
Vienna RNAfold output file [rna1.vrnaplot]:


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Plot vrnafold output
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-structuresfile]    infile     Vienna RNAfold output file
  [-outfile]           outfile    [*.vrnaplot] Vienna RNAfold output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -layout             menu       [naview] Layout (Values: radial (Simple
                                  radial); naview (naview))
   -optype             menu       [ps] Type (Values: ps (postscript); gml
                                  (graph meta language); svg (scaleable vector
                                  graphics); xrna (XRNA save file))
   -pre                string     Pre-annotation (Any string)
   -post               string     Post-annotation (Any string)

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


Input file format

   vrnaplot reads any normal sequence USAs.

  Input files for usage example

  File: ../vrnafold-keep/rna1.vrnafold

CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA
.(((..((....)).(((((........)))))..))).. ( -3.50)

Output file format

   vrnaplot outputs a graph to the specified graphics device. outputs a
   report format file. The default format is ...

  Output files for usage example

  Graphics File: rna1.vrnaplot

   [vrnaplot results]

Data files

   For details of Vienna RNA file formats, see the original documentation
   http://www.tbi.univie.ac.at/~ivo/RNA/

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

                     Program name                       Description
                    einverted      Finds inverted repeats in nucleotide sequences
                    vrnaalifold    RNA alignment folding
                    vrnaalifoldpf  RNA alignment folding with partition
                    vrnacofold     RNA cofolding
   vrnacofoldconc   RNA cofolding with concentrations
                    vrnacofoldpf   RNA cofolding with partitioning
                    vrnadistance   RNA distances
                    vrnaduplex     RNA duplex calculation
                    vrnaeval       RNA eval
                    vrnaevalpair   RNA eval with cofold
                    vrnafold       Calculate secondary structures of RNAs
                    vrnafoldpf     Secondary structures of RNAs with partition
                    vrnaheat       RNA melting
                    vrnainverse    RNA sequences matching a structure
                    vrnalfold      Calculate locally stable secondary structures of RNAs
                    vrnasubopt     Calculate RNA suboptimals

Author(s)

   Peter            Rice (pmr (c) ebi.ac.uk)
   European         Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton,         Cambridge CB10 1SD, UK

History

                    Converted (October 2005) by Alan Bleasby

Target users

                    This program is intended to be used by everyone and everything, from
                    naive users to embedded scripts.

Comments
