The GCG programs represent nucleotides and ambiguities in sequence using the IUB symbols. The Staden symbols are included for comparison:
IUB/GCG Nucleotide Staden/Sanger
symbol meaning symbol
A A A
C C C
G G G
T/U T U
M A or C 5
R A or G R
W A or T 7
S C or G 8
Y C or T Y
K G or T 6
V A or C or G not supported
H A or C or T not supported
D A or G or T not supported
B C or G or T not supported
X/N G or A or T or C -/X
Frame ambiguity symbols are used in the Staden system. These are not supported by GCG, but are translated by FROMSTADEN as the lower case, single letter, equivalent.
Staden code Meaning GCG
D C or CC c
V T or TT t
B A or AA a
H G or GG g
K C or CX c
L T or TX t
M A or AX a
N G or GX g
BE CAREFUL when interchanging formats - as the letters DVBHN in Staden have different meanings in GCG.