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MEME accepts DNA or protein sequences. The sequences must all be of the same type, either protein or DNA. DNA sequences are not translated into protein.

• Protein sequences should use the standard IUPAC alphabet: ACDEFGHIKLMNPQRSTVWY.
  In addition, the following conversions from ambiguous to unambiguous letter codes are made automatically by MEME for protein sequences:
  
  • B --> D (Asp, Asn to Asp)
  • U --> C (selenocysteine to cysteine)
  • X --> C (unknown to cysteine)
  • Z --> E (Glu, Gln to Glu)

• DNA sequences should use the standard DNA alphabet: ACGT.
  In addition, the following conversions from ambiguous to unambiguous letter codes are made automatically by MEME for DNA sequences:
  
  • B --> C (GTC to C)
  • D --> G (GAT to G)
  • H --> A (ACT to A)
  • K --> T (GT to T)
  • M --> A (AC to A)
  • N --> C (any to C)
  • R --> A (GA to A)
  • S --> G (GC to G)
  • U --> T (uridine to T)
  • V --> G (GCA to G)
  • W --> T (AT to T)
  • Y --> C (TC to C)

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