showorf displays a nucleic acid sequence with its protein translation in a style suitable for publication. The translation can be done in any frame or combination of frames.

Here is a sample session with showorf:

% showorf
Pretty output of DNA translations
Input sequence: embl:paamir
Select Frames To Translate
         0 : None
         1 : F1
         2 : F2
         3 : F3
         4 : R1
         5 : R2
         6 : R3
Select one or more values [1,2,3,4,5,6]:
Output file [paamir.showorf]:

Mandatory qualifiers:

[-sequence] (sequence)

Sequence USA.

-frames (menu)

Select one or more values.

[-outfile] (outfile)

Output filename.

Optional qualifiers:

-[no]ruler (boolean)

Add a ruler.

-[no]plabel (boolean)

Number translations.

-[no]nlabel (boolean)

Number DNA sequence.

Advanced qualifiers:

-cfile (codon)

Codon usage file.

-width (integer)

Width of screen.