MEME accepts DNA or protein sequences. The sequences must all be of the same type, either protein or DNA.
- Protein sequences should use the standard IUPAC alphabet: ACDEFGHIKLMNPQRSTVWY.
They may also contain the ambiguous letters "BUXZ", which MEME converts to "X" and treats as "unknown".
- DNA sequences should use the standard DNA alphabet: ACGT.
They may also contain the ambiguous letters "BDHKMNRSUVWY", which MEME converts to "X" and treats as "unknown".
Note: If none of the sequences in your dataset contain any of the letters "EFILPQXZ", MEME will assume your sequences are DNA. You can force MEME to interpret them as protein sequences by adding an "X" to the end (or beginning) of one of the sequences in your dataset.