Base pair encoding
wmf at LARIAT.LANL.GOV
Mon Jul 1 17:28:58 EST 1991
Michael Kosowsky asks:
>>How do GENBANK and NCBI's GENINFO symbolize uncertain base pairs?
>>I've so far learned of three incompatible systems.
>>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:
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:
Hope this helps.
-- Will Fischer
(Working at GenBank, but speaking for myself)
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