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

[Eric Talevich]

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:
http://www.uga.edu/RNA-Informatics/files/software/RNApasta.help.html#Format

I'm not sure how standardized or widely used it is, but the program
RNA-pasta works with it:
http://www.uga.edu/RNA-Informatics/?f=software&p=RNApasta

-Eric