The first module you use on the Design a Gene path is Reverse Translation. This is where you will input your protein sequence and choose the codons that will be used in the nucleotide sequence. A single codon will be assigned to each amino acid by default. GeneDesign does not allow multiple codons to be assigned to the sequence at this stage of the gene design.
First, paste your sequence in amino acids into the text area at top.
The Reverse Translation Module
To define the codon usage you can select one
of the four common organisms from the radio buttons. (A) Choosing
an organism will cause the pop-up boxes to automatically select the codon
with the highest RSCU value in highly expressed genes in that organism (pubmed).
You can then edit the selection if you wish.
You may also paste your own custom codon table into (B).
The format is "AA space codon line break",
so that the first line of a valid table could be "M ATG" and the
second line "L
CTG", for example. Any input in the codon table will supercede entries
in the pop-up boxes. Your 21 codon input will be labeled the optimal codons.
This version of GeneDesign uses the standard genetic code.
Once the codons have been defined to your satisfaction, hit "Reverse Translate".
Your new nucleotide sequence will appear. There will be several buttons
at the bottom that allow you to take this nucleotide sequence to other
modules. To follow the Design a Gene path, click "Silent
Site Insertion".