[Biococoa-dev] Subclassing BCSequence really needed?

[John Timmer]

>>> There's two other reasons I favor this structure:  What you tend to
>>> do with
>>> DNA sequences and what you tend to do with protein sequences are
>>> typically
>>> very different - I don't see why they all the differences should be
>>> forced
>>> to reside in the same class.
>> 
>> They shouldn't be, although I fail to understand why getting a
>> subsequence is different for a DNA or protein. But that might be
>> because of my limited knowledge of the biology.

If you're asking for the range of a subsequence (which is what the methods I
was referring to do), then there is  a difference.  With amino acids,
there's no ambiguity - what you ask for is what you find.  With nucleotides,
what happens if you ask for GARNYTC?  You could either be asking for an
exact match, in which case the same method as with amino acids would work.
Or you could be asking for any sequence that might match that, such as
GAAACTC and GAGGCTC etc.  Clearly, you need a second method for that.
There's situations where you'd want one or the other (or at least I would),
so it's definitely worth providing both.

Cheers,

JT


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