EMBOSS

1. Save all sequences in one flatfile format (NOT MacVector format), e.g. genbank format.
2. Copy all sequences to a Linux/UNIX computer and convert them from Mac format to UNIX format: mac2unix *.gb
3. Write all sequence fiule names into one file: ls *.gb > oligo.lst
4. Convert all sequences into one file of concatenated fasta entries using EMBOSS: seqret -sequence @oligo.lst -osformat fasta. Call the output file "mcbl_oligo_db"
5. Put this fasta file into the blast web servers database directory (.../blast/db)

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 detects also more complex changes is a web tool: WatCut.