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

Peter biopython at maubp.freeserve.co.uk
Wed Jun 2 09:23:15 UTC 2010

On Tue, Jun 1, 2010 at 7:25 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> I could be totally wrong here, but I think it's useful to lay out some
> assumptions and intuitions explicitly.
> To me, secondary structure is not really a separate dimension in its own
> right, the way tertiary structure corresponds to 3D space and primary
> structure corresponds to a linear sequence. Instead, secondary structure has
> meaning in 3D space, but is usually serialized as a linear sequence. That
> is, we want to parse something that resembles a sequence, but be able to map
> it onto a 3D structure. (More for proteins than for RNA, usually.)
> (For non-RNA folk, here's an example of RNA secondary structure:
> http://github.com/krother/biopython/blob/rna/Tests/RNA/sample.vienna
> )
> For instance, the output of DSSP and Jpred describes a protein's secondary
> structure, but the input to DSSP is a 3D structure, while Jpred accepts a
> protein sequence. The representation of secondary structure isn't distinct
> from either of these. I'd want both of these available in Bio.Struct
> (eventually).
> This means that some interaction between Bio.Struct and SeqIO is necessary.
> It would be neat if secondary structure regions were represented as
> SeqFeature instances, and secondary-structure parsers returned some kind of
> subclass of SeqRecord -- or a standard SeqRecord containing a special kind
> of Seq.
> ...
> 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.


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