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)