[Biopython] Sequence object "find" is still case specific?

[Michiel de Hoon]

> Hmm, well, lower case nucleotides have often represented
> "masked regions" of sequences. It seems that Biopython
> sequences were meant to be case-sensitive (e.g.,
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc22).
> From the documentation there, it seems like you've discovered
> a bug in the API; I feel that Seq should raise a ValueError
> when instantiating with lower-case nucleotides and unambiguous_dna.
> 
I don't think that this is a bug. The difference between unambiguous and ambiguous DNA refers to the difference between ACGT and ACGTMRWSYKVHDBXN,
where the nucleotides other than ACGT are ambiguous (for example, R = purine = either A or G).

Best,
-Michiel.