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.

Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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