# MEME Suite Alphabets

- The two IUPAC 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.