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 
AAlanine
CCysteine
DAspartic acid
EGlutamic acid
FPhenylalanine
GGlycine
HHistidine
IIsoleucine
KLysine
LLeucine
MMethionine
NAsparagine
PProline
QGlutamine
RArginine
SSerine
TThreonine
VValine
WTryptophan
YTyrosine
Symbol(s)NameMatches
X * .Any amino acidA C D E F G H I K L M N P Q R S T V W Y
BAsparagine or Aspartic acidD N
ZGlutamine or Glutamic acidE Q
JLeucine or IsoleucineI 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)NameComplement
AAdenineT
CCytosineG
GGuanineC
T UThymineA
Symbol(s)NameMatches
N . XAny baseA C G T
VNot TA C G
HNot GA C T
DNot CA G T
BNot AC G T
MAminoA C
RPurineA G
WWeakA T
SStrongC G
YPyrimidineC T
KKetoG 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 
AAdenine
CCytosine
GGuanine
U TUracil
Symbol(s)NameMatches
N . XAny baseA C G U
VNot UA C G
HNot GA C U
DNot CA G U
BNot AC G U
MAminoA C
RPurineA G
WWeakA U
SStrongC G
YPyrimidineC U
KKetoG U