IUPAC Codes

IUPAC Nucleotide Code

IUPAC nucleotide code	Base
A	Adenine
C	Cytosine
G	Guanine
T (or U)	Thymine (or Uracil)
R	A or G
Y	C or T
S	G or C
W	A or T
K	G or T
M	A or C
B	C or G or T
D	A or G or T
H	A or C or T
V	A or C or G
N	any base

IUPAC Amino Acid Code

IUPAC amino acid code	Three letter code	Amino acid
A	Ala	Alanine
C	Cys	Cysteine
D	Asp	Aspartic Acid
E	Glu	Glutamic Acid
F	Phe	Phenylalanine
G	Gly	Glycine
H	His	Histidine
I	Ile	Isoleucine
K	Lys	Lysine
L	Leu	Leucine
M	Met	Methionine
N	Asn	Asparagine
P	Pro	Proline
Q	Gln	Glutamine
R	Arg	Arginine
S	Ser	Serine
T	Thr	Threonine
V	Val	Valine
W	Trp	Tryptophan
Y	Tyr	Tyrosine

RNA Structural Constraint Notation

symbol	meaning
(	nucleotide must be base paired (upstream)
)	nucleotide must be base paired (downstream, paired to upstream)
.	no constraint, nucleotide may/may not be base paired
x	nucleotide may not be base paired

Examples

An RNA hairpin containing a 5-nucleotide duplex and a 4-nucleotide hairpin loop.

(((((xxxx)))))

An RNA hairpin containing a 5-nucleotide duplex, an essential internal loop, and a 6-nucleotide hairpin loop.

(((x((xxxxxx))x)))

An RNA cloverleaf containing 3 branches and assorted bulges, internal loops, and hairpin loops. Some are essential and others not.

(((((xx(((((..xx..((((((.xxx.))).)))xx(((xx((..xxxx..))xx))).....((x(((((((.xxx.)))))))))xxxx))))))))))...