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

Eric Talevich eric.talevich at gmail.com
Thu Jun 3 16:17:09 UTC 2010

On Wed, Jun 2, 2010 at 8:14 AM, Kristian Rother <krother at rubor.de> wrote:

> 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 '(((..[[[....)))..]]]'.
Here's another format that was designed to represent pseudoknots:

I'm not sure how standardized or widely used it is, but the program
RNA-pasta works with it:


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