[Biopython-dev] upcoming Bio.PDB enhancements - RNA

Kristian Rother krother at rubor.de
Wed Jun 2 12:14:05 UTC 2010

Hi Peter,

Bio.SeqIO would be a nice place for RNA 2D parsers. I can create a new
branch for that (on Git: krother/biopython).

Putting secondary structures like '((((....))))' for a hairpin into the
letter_annotation field makes sense. I think it even would work for
pseudoknotted RNA (which is hard to represent as a string, one possible
notation would be '(((..[[[....)))..]]]'.

Where should the str subclass for secondary structures that the parsers
create go? Could it be Bio.Struct.RNA?


Putting RNA secondary structures
>> As for protein secondary structure, it's usually associated with a
>> sequence
>> or a structure, so maybe we could get by with storing that information
>> in an
>> ordinary Structure or SeqRecord object without inventing a new subclass.
> Maybe all/most secondary structure parsers can just go into Bio.SeqIO (for
> both proteins, RNA and DNA). We can store a secondary structure string as
> per-letter-annotation, or things like helix regions as SeqFeature objects.
> Peter

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