Thanks,
I will think about it some more. In general, I am much more concerned with
usability and correctness than effeciency, but I certainly won't turn down
effeciency gains if they are just sitting there. If I end up just storing DNA
as an int array and then, for most uses, convert it back to a string, will
that actually gain anything?

The biggest Regex need is shown below. I do use some other Regex's, but this
is the one I don't think I could really replace. I guess I can always convert
to a string and then create the Regex from that is need be.
Ethan

    /// <summary>
       /// Creates a regular expression of all sequences which could code
for a specific amino acid Sequence
       /// </summary>
       /// <param name="residues">A string containing the amino acid
Sequence</param>
       /// <returns>a string which represents the Regular
expression</returns>
       public static string BackTranslateToRegex(string residues)
       {
           if (residues == null)
           {
               throw new ArgumentNullException("residues", "you need a
Sequence from which to make a regex.");
           }
           Hashtable BackTranslations = new Hashtable();
           BackTranslations.Add('*', "T(GA|A[GA])");
           BackTranslations.Add('A', "GC[GATC]");
           BackTranslations.Add('C', "TG[TC]");
           BackTranslations.Add('D', "GA[TC]");
           BackTranslations.Add('E', "GA[GA]");
           BackTranslations.Add('F', "TT[TC]");
           BackTranslations.Add('G', "GG[GATC]");
           BackTranslations.Add('H', "CA[TC]");
           BackTranslations.Add('I', "AT[ATC]");
           BackTranslations.Add('K', "AA[GA]");
           BackTranslations.Add('L', "(TT[GA]|CT[GATC])");
           BackTranslations.Add('M', "ATG");
           BackTranslations.Add('N', "AA[TC]");
           BackTranslations.Add('P', "CC[GATC]");
           BackTranslations.Add('Q', "CA[GA]");
           BackTranslations.Add('R', "(AG[GA]|CG[GATC])");
           BackTranslations.Add('S', "(AG[TC]|TC[GATC])");
           BackTranslations.Add('T', "AC[GATC]");
           BackTranslations.Add('V', "GT[GATC]");
           BackTranslations.Add('W', "TGG");
           BackTranslations.Add('Y', "TA[TC]");
           StringBuilder Expression = new StringBuilder();
           char[] Residues = residues.ToCharArray();
           foreach (char Residue in Residues)
           {
               Expression.Append(BackTranslations[Residue]);
           }
           return Expression.ToString();
       }