EMBOSS: plotorf

| ## 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