
                              EMBOSS: plotorf
     _________________________________________________________________
   
                                Program plotorf
                                       
Function

   Plot potential open reading frames
   
Description

   Plot potential open reading frames.
   
   A graphical representation of where the open reading frames are in all
   6 reading frames is shown. The ORFs are displayed as blue boxes.
   
   ORFs in this program are defined as being regions between START and
   STOP codons.
   
   Note that this definition of an ORF would miss those exons in
   eukaryotic genomic sequences which do not contain a START codon.
   plotorf is only really useful when dealing with prokaryotic or mRNA
   eukaryotic sequences.
   
   The default START codon is: "ATG".
   The default STOP codons are: "TAA,TAG,TGA".
   
   You can specify your own set of start and stop codons using the -start
   and -stop qualifiers.
   
Usage

   Here is a sample session with plotorf.
   
% plotorf
Plot potential open reading frames
Input sequence: embl:paamir
Graph type [x11]:

   Click here to see the graph
   
   An example of specifying your own START and STOP codons with a
   mitochondrial sequence would be:
   
% plotorf -start ATT,ATC,ATA,ATG,GTG -stop TAA,TAG,AGA,AGG
Plot potential open reading frames
Input sequence: mito.seq
Graph type [x11]:

Command line arguments

   Mandatory qualifiers:
  [-sequence]          sequence   Sequence USA
   -graph              xygraph    Graph type

   Optional qualifiers: (none)
   Advanced qualifiers:
   -start              string     Start codons
   -stop               string     Stop codons

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence USA Readable sequence Required
   -graph Graph type EMBOSS has a list of known devices, including
   postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows,
   x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm,
   png EMBOSS_GRAPHICS value, or x11
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -start Start codons Any string is accepted ATG
   -stop Stop codons Any string is accepted TAA,TAG,TGA
   
Input file format

   Any nucleic acid sequence.
   
Output file format

   Graphical output.
   
Data files

   None.
   
Notes

   ORFs in this program are defined as being regions between START and
   STOP codons.
   
   Note that this definition of an ORF would miss those exons in
   eukaryotic genomic sequences which do not contain a START codon.
   plotorf is only really useful when dealing with prokaryotic or mRNA
   eukaryotic sequences.
   
References

   None.
   
Warnings

   See the Notes section.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with a status of 0.
   
Known bugs

   None.
   
See also

   Program name                          Description
   backtranseq  Back translate a protein sequence
   coderet      Extract CDS, mRNA and translations from feature tables
   getorf       Finds and extracts open reading frames (ORFs)
   marscan      Finds MAR/SAR sites in nucleic sequences
   prettyseq    Output sequence with translated ranges
   remap        Display a sequence with restriction cut sites, translation etc
   showorf      Pretty output of DNA translations
   showseq      Display a sequence with features, translation etc
   transeq      Translate nucleic acid sequences
   wobble       Wobble base plot
   
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
History

   Written (1999) - Alan Bleasby
   
Target users

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