GeneDesign's Reverse Translation module takes a protein sequence to synonymous nucleotide sequence using either a user-defined codon scheme or the most optimal codons for expression in a user-selected organism.
The Reverse Translation Module
To define the codon usage you can select one
of the four common organisms from the radio buttons. 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 the program.
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 all entries
in the pop-up boxes, so your table must be complete. Your 21 codon input
will be used as 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.