# The MEME Suite

## Motif-based sequence analysis tools

### Alphabets

The two IUPAC alphabets are allowed.

#### Protein Alphabet

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

#### DNA Alphabet

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)

#### Other

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.