GeneDesign's Silent Site Removal module allows you to remove restriction enzyme sites without affecting the translation of the sequence.
After you input your sequence, GeneDesign will parse it for restriction sites and report back to you with a list of all of the present sites. You can check as many as you like for removal and GeneDesign will attempt to remove them all. If you defined a host organism, codon changes will be made with the optimization of the sequence in mind. If no organism was defined all changes will be random. Any errors or difficulties will be reported to you on the last page, as well as the similarity of the new sequence to the old sequence.
After site removal you can take the sequence to another module.