Shortcoming of silent mutagenesis tools (EMBOSS, GCK): WatCut as a solution

Update: As of May 2026, the last functional instance of the WatCut web service (by the University of Pittsburgh) was discontinued. However, tools like Snapgene ( https://snapgene.com  ) have the same functionality (i.e. can detect novel restriction sites by silent mutagenesis of two nucleotides).

Many programs that try to detect possible restriction sites in nucleotide sequences while maintaining the protein sequence fail big time. Because the genetic code is degenerate you can by silent mutation change the nucleotide sequence while maintaining the protein sequence. However, most programs that aim to identify those possible silent changes look only for single nucleotide substitutions (e.g. EMBOSS, GCK2.5, etc.). The only program that seems to detect also more complex changes is a web tool: WatCut  .