plotorf

Function

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

Command line arguments


Input file format

Any nucleic acid sequence.

Output file format

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.

Author(s)

History

Target users

Comments