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Nucleotide ambiguity code
(IUPAC)
Nucleotide ambiguity code
(as defined in DNA Sequence Assembler)
|
Code
|
Represents
|
Complement
|
A
|
Adenine
|
T
|
G
|
Guanine
|
C
|
C
|
Cytosine
|
G
|
T
|
Thymine
|
A
|
Y
|
Pyrimidine (C or T)
|
R
|
R
|
Purine (A or G)
|
Y
|
W
|
weak (A or T)
|
W
|
S
|
strong (G or C)
|
S
|
K
|
keto (T or G)
|
M
|
M
|
amino (C or A)
|
K
|
D
|
A, G, T (not C)
|
H
|
V
|
A, C, G (not T)
|
B
|
H
|
A, C, T (not G)
|
D
|
B
|
C, G, T (not A)
|
V
|
|
X/N
|
any base
|
X/N
|
-
|
Gap
|
-
|
|
|
Code example:
Restriction enzyme: AarI
Recognition site: CACCTGCNNNN'NNNN_
Cleavage of DNA (/):
5'- C A C C T G C N N N N/N N N N -3'
3'- G T G G A C G N N N N N N N N/-5'
The letter codes and compliment translations are those proposed by Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-UIBMB)
Note:
DNA Sequence Assembler can automatically detect SNP and convert them to IUPAC codes. Its Reverse Complement tool can also automatically reverse complement IUPAC bases.
|
Standard Ambiguity Codes
The standard ambiguity codes for nucleotides and for the one-letter and three-letter designations of amino acids are given. The synonymous codons for the amino acids, and their depiction
in IUB codes (Nomenclature Committee, 1985, Eur. J. Biochem. 150:1-5) are also shown.
Nucleotide |
Symbol |
3-Let |
Amino Acid |
IUB |
(Adenosine) A |
A |
Ala |
Alanine |
GCX |
C or G or T/U |
B |
Asx |
Aspartate or Asparagine |
RAY |
(Cytidine) C |
C |
Cys |
Cysteine |
UGY |
A or G or T/U |
D |
Asp |
Aspartate |
GAY |
- |
E |
Glu |
Glutamate |
GAR |
- |
F |
Phe |
Phenylalanine |
UUY |
(Guanosine) G |
G |
Gly |
Glycine |
GGX |
A or C or T/U |
H |
His |
Histidine |
CAY |
(Inosine) I |
I |
Ile |
Isoleucine |
AUH |
- |
J |
- |
- |
- |
G or T/U |
K |
Lys |
Lysine |
AAR |
- |
L |
Leu |
Leucine |
UUR,CUX,YUR |
A or C |
M |
Met |
Methionine |
AUG |
unknown base |
N |
Asn |
Asparagine |
AAY |
- |
O |
- |
- |
- |
- |
P |
Pro |
Proline |
CCX |
- |
Q |
Gln |
Glutamine |
CAR |
(Purine) A or G |
R |
Arg |
Arginine |
CGX,AGR,MGR |
C or G |
S |
Ser |
Serine |
UCX,AGY |
(Thymidine) T |
T |
Thr |
Threonine |
ACX |
(Uridine) U |
U |
- |
- |
- |
A or C or G |
V |
Val |
Valine |
GUX |
A or T/U |
W |
Trp |
Tryptophan |
UGG |
unknown base |
X |
unknown amino acid |
|
XXX |
(Pyrimidine)
C or T/U |
Y |
Tyr |
Tyrosine |
UAY |
- |
Z |
Glx |
Glutamate or Glutamine |
SAR |
no base (deletion/gap) |
. |
no amino acid (deletion/gap) |
- |
- |
- |
* |
End |
terminator |
UAR,URA |
How the standard ambiguity codes were assigned |
Standard Amino Acid Codes
A = Ala = Alanine
C = Cys =Cysteine (not Cystine!)
G = Gly = Glycine
I = Ile =Isoleucine
L = Leu = Leucine
M = Met = Methionine
P = Pro = Proline
S = Ser = Serine
T = Thr = Threonine
V = Val = Valine
should be obvious codes |
Standard Nucleotide Codes
A = Adenylic acid
C = Cytidylic acid
G = Guanylic acid
T = Thymidylic acid
U = Uridylic acid
I = Inosylic acid
should be obvious codes |
F = Phe = Phenylanine
N = Asn = Asparagine
R = Arg = Arginine
Y = Tyr = Tyrosine
are phonetic codes |
R = A or G = puRine
Y = C or T = pYrimidine
K = G or T = Keto
M = A or C = aMino
S = G or C = Strong base pair
W = A or T = Weak base pair
double base codes |
D = Asp = Aspartic acid
E = Glu = Glutamic acid
K = Lys = Lysine
Q = Gln = Glutamine
W = Trp = Tryptophan (big letter big residue)
non-obvious codes (you just have to learn them!) |
B = not A (G or C or T)
D = not C (A or G or T)
H = not G (A or C or T)
V = not T/U (A or C or G)
triple base codes |
B = Asx = Aspartic acid or Asparagine
Z = Glx = Glutamic acid or Glutamine
these are ambiguity codes |
N = aNy base (by convention, X is used for unknown amino acids, N for unknown nucleotides)
|
X = any amino acid
J, O, U = no amino acid codes
.(dot) = deletion or gap
*(star) = End or terminator
|
E, F, J, L, O, P, Q, Z
have no base codes
.(dot) = deletion or gap
|
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