DNA Ambiguity codes

N = A or C or G or T (any)
B = C or G or T (not A)
D = A or G or T (not C)
H = A or C or T (not G)
V = A or C or G (not T)
W = A or T (weak)
S = C or G (strong)
R = A or G (purine)
Y = C or T (pyrimidine)
M = A or C (amino)
K = G or T (keto)

The Single-Letter Amino Acid Code

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

Prosite patterns

• The standard IUPAC one-letter codes for the amino acids are used.
• The symbol ‘x’ is used for a position where any amino acid is accepted.
• Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses ‘[ ]’. For example: [ALT] stands for Ala or Leu or Thr.
• Ambiguities are also indicated by listing between a pair of curly brackets ‘{ }’ the amino acids that are not accepted at a given position. For example: {AM} stands for any amino acid except Ala and Met.
• Each element in a pattern is separated from its neighbor by a ‘-’.
• Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to x-x or x-x-x or x-x-x-x.
• When a pattern is restricted to either the N- or C-terminal of a sequence, that pattern either starts with a ‘<’ symbol or respectively ends with a ‘>’ symbol. In some rare cases (e.g. PS00267 or PS00539), ‘>’ can also occur inside square brackets for the C-terminal element. ‘F-[GSTV]-P-R-L-[G>]’ means that either ‘F-[GSTV]-P-R-L-G’ or ‘F-[GSTV]-P-R-L>’ are considered.
• A period ends the pattern.