# The MEME Suite

## Motif-based sequence analysis tools

## Standard Alphabets

The MEME Suite supports 3 standard alphabets: protein, DNA and RNA.

If none of these alphabet are suitable you may also define custom alphabets.

### Protein Alphabet

The protein alphabet contains twenty characters for amino acids 'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y' and is augmented by four more ambiguous characters 'X', 'B', 'Z' and 'J'. There are two aliases for the wildcard 'X'; '*' which would normally represent a stop codon and '.' which would normally represent a gap.

Symbol(s) | Name |
--- | --- | ---
A | Alanine |
C | Cysteine |
D | Aspartic acid |
E | Glutamic acid |
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 |
V | Valine |
W | Tryptophan |
Y | Tyrosine |
Symbol(s) | Name | Matches
X * . | Any amino acid | A C D E F G H I K L M N P Q R S T V W Y
B | Asparagine or Aspartic acid | D N
Z | Glutamine or Glutamic acid | E Q
J | Leucine or Isoleucine | I L

### DNA Alphabet

The MEME Suite uses the standard 4 symbol alphabet 'A', 'C', 'G', 'T' for DNA but also accepts the RNA symbol 'U' as an alias for 'T'. In addition there are 11 ambiguous symbols 'N', 'V', 'H', 'D', 'B', 'M', 'R', 'W', 'S', 'Y', and 'K'. There are 2 aliases for the wildcard 'N'; '.' as the MEME Suite does not support gaps but it is sometimes necessary to ignore them and 'X' because MEME used to use it for masking no matter what the sequence alphabet was.

Symbol(s) | Name | Complement
--- | --- | ---
A | Adenine | T
C | Cytosine | G
G | Guanine | C
T U | Thymine | A
Symbol(s) | Name | Matches
N . X | Any base | A C G T
V | Not T | A C G
H | Not G | A C T
D | Not C | A G T
B | Not A | C G T
M | Amino | A C
R | Purine | A G
W | Weak | A T
S | Strong | C G
Y | Pyrimidine | C T
K | Keto | G T

### RNA Alphabet

The MEME Suite uses the standard 4 symbol alphabet 'A', 'C', 'G', 'U' for RNA but also accepts the DNA symbol 'T' as an alias for 'U'. In addition there are 11 ambiguous symbols 'N', 'V', 'H', 'D', 'B', 'M', 'R', 'W', 'S', 'Y', and 'K'. There are 2 aliases for the wildcard 'N'; '.' as the MEME Suite does not support gaps but it is sometimes necessary to ignore them and 'X' because MEME used to use it for masking no matter what the sequence alphabet was.

Symbol(s) | Name |
--- | --- | ---
A | Adenine |
C | Cytosine |
G | Guanine |
U T | Uracil |
Symbol(s) | Name | Matches
N . X | Any base | A C G U
V | Not U | A C G
H | Not G | A C U
D | Not C | A G U
B | Not A | C G U
M | Amino | A C
R | Purine | A G
W | Weak | A U
S | Strong | C G
Y | Pyrimidine | C U
K | Keto | G U