[BioSQL-l] Recording "nucleotide" in the sequence table?

[Hilmar Lapp]

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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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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