Michael Kosowsky asks:
>>How do GENBANK and NCBI's GENINFO symbolize uncertain base pairs?
>>I've so far learned of three incompatible systems.
>>(Stuff deleted)
>>I naively hope to get away with implementing just one.
The standard code was defined in Cornish-Bowden,A. (1985) Nucl Acid Res 13,
3021-3030. GenBank uses it, as should all right-thinking sequence programs.
I. Ambiguous assignments are represented as follows:
symbol meaning
a a
g g
c c
t t
r a or g
y c or t
m a or c
k g or t
s c or g
w a or t
h a or c or t
b c or g or t
v a or c or g
d a or g or t
n a or c or g or t
II. Base complementary relationships are as follows:
symbol complement
a t
b v
c g
d h
g c
h d
k m
m k
s s
t a
v b
w w
n n
Hope this helps.
-- Will Fischer
(Working at GenBank, but speaking for myself)
