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").
| Symbol | Meaning |
|---|---|
| A | alanine |
| B | aspartate or asparagine |
| C | cystine |
| D | aspartate |
| E | glutamate |
| F | phenylalanine |
| G | glycine |
| H | histidine |
| I | isoleucine |
| K | lysine |
| L | leucine |
| M | methionine |
| N | asparagine |
| P | proline |
| Q | glutamine |
| R | arginine |
| S | serine |
| T | threonine |
| U | any |
| V | valine |
| W | tryptophan |
| Y | tyrosine |
| Z | glutamate or glutamine |
| X | any |
The four-character DNA alphabet ("ACGT") is augmented by eleven ambiguous characters ("RYKMSWBDHVN"). The RNA alphabet code for uracil ("U") is also accepted but it is converted to T for processing.
| Symbol | Meaning |
|---|---|
| A | adenosine |
| C | cytidine |
| G | guanine |
| T | thymidine |
| U | uracil (MEME Suite converts to T) |
| R | G A (purine) |
| Y | T C (pyrimidine) |
| K | G T (keto) |
| M | A C (amino) |
| S | G C (strong) |
| W | A T (weak) |
| B | G T C |
| D | G A T |
| H | A C T |
| V | G C A |
| N | A G C T (any) |
Any other characters (digits, punctuation, etc.) are illegal. The typical behavior of MEME Suite programs is to skip any sections of sequence that contain these.