[BioSQL-l] Recording "nucleotide" in the sequence table?
Hilmar Lapp
hlapp at gmx.net
Sat May 16 22:10:43 UTC 2009
I think we'll have to define carefully what we mean by "generic
nucleotide alphabet". (Normally I hear nucleotide used as the type of
a sequence, but not its alphabet.)
A nucleotide alphabet in the way you describe it also can't really be
the "base class" for either a DNA or RNA alphabet, can it? Typically
in OOP, derived classes expand on a base class, not restrict it. So
isn't there potential for confusion?
What you are essentially talking about is the case when a sequence
contains only A, C, and G. In that case, we don't know either that
it's not protein, do we?
> [...] In python "guessing" is discouraged. If we have a nucleotide
> sequence
> like GCGCGCGA, this could be DNA or RNA - you can't tell.
And how do you tell it's nucleotide to begin with?
-hilmar
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