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

Peter biopython at maubp.freeserve.co.uk
Wed Jun 2 13:24:49 UTC 2010

On Wed, Jun 2, 2010 at 1:14 PM, Kristian Rother <krother at rubor.de> wrote:
> 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?
> Best,
>   Kristian

You don't think plain strings in the SeqRecord's letter_annotation
dict would be enough? Assuming you do need something then
perhaps under Bio.Seq or Bio.SeqUtils might be worth considering
as alternatives to Bio.Struct.RNA.


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