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                boolean    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 nameDescription
backtranseqBack translate a protein sequence
coderetExtract CDS, mRNA and translations from feature tables
getorfFinds and extracts open reading frames (ORFs)
marscanFinds MAR/SAR sites in nucleic sequences
prettyseqOutput sequence with translated ranges
remapDisplay a sequence with restriction cut sites, translation etc
showorfPretty output of DNA translations
showseqDisplay a sequence with features, translation etc
transeqTranslate nucleic acid sequences
wobbleWobble 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.

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