[Biopython-dev] New Biopython release coming up / Alphabets

Michiel Jan Laurens de Hoon mdehoon at c2b2.columbia.edu
Thu Jul 6 16:39:09 UTC 2006

Michael Hoffman wrote:
> [Peter]
>> But to be honest, I have generally used plain strings in my own
>> programs, and meddled with alphabets only when needed (e.g. for
>> translating from DNA to protein sequences).

Note that there is a function "translate" in Bio.Seq that translates DNA 
to protein using plain strings.
> I agree. In general, I think that the alphabet stuff adds unnecessary
> complexity to perhaps 95 % of the sort of things I would do with
> Biopython. But as it stands I usually use strs myself instead.

It appears that most people (myself included) use plain strings instead 
of Seq objects (= string + Alphabet). We should check on the biopython 
mailing list if anybody really needs alphabets, and if not get rid of 
them (after the upcoming Brooklyn-release (1.42) though).


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue
New York, NY 10032

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