Alphabets

• Two alphabets are allowed.
  • The protein alphabet contains twenty characters for amino acids ("ACDEFGHIKLMNPQRSTVWY"), and is augmented by four more ambiguous characters ("BUXZ").

        A  alanine                         P  proline
        B  aspartate or asparagine         Q  glutamine
        C  cystine                         R  arginine
        D  aspartate                       S  serine
        E  glutamate                       T  threonine
        F  phenylalanine                   U  any
        G  glycine                         V  valine
        H  histidine                       W  tryptophan
        I  isoleucine                      Y  tyrosine
        K  lysine                          Z  glutamate or glutamine
        L  leucine                         X  any
        M  methionine                      
        N  asparagine
    

  • The four-character DNA alphabet ("ACGT") is augmented by eleven ambiguous characters:

        A --> adenosine                 M --> A C (amino)
        C --> cytidine                  S --> G C (strong)
        G --> guanine                   W --> A T (weak)
        T --> thymidine                 B --> G T C
                                        D --> G A T
        R --> G A (purine)              H --> A C T
        Y --> T C (pyrimidine)          V --> G C A
        K --> G T (keto)                N --> A G C T (any)
    

• Any other characters (digits, punctuation, etc.) are illegal.

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