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plotorf |
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.
% plotorf Plot potential open reading frames Input sequence: embl:paamir Graph type [x11]:
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]:
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 |
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.
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 |