Topics

1

RNA structures (DSSR) / Lost info in CT output

« on: November 02, 2014, 10:19:43 am »

Hello Xiang-Jun,

first of all, I think you will be glad that we cited DSSR in our poster at BIBM 2014 (Template-Based Prediction of Ribosomal RNA Secondary Structure), currently hanging on a panel in Belfast and to be published in the Workshop & Poster proceedings.

I have, however, run into a problem: in CT format, on PDB entry 4CXC, the '#' sign and descriptors to the right of it are missing. We do miss them. Is there an option to turn them back on?

Thanks!

Jan Hajic

2

RNA structures (DSSR) / Higher-order pseudoknots in DP output

« on: May 11, 2014, 03:43:44 pm »

Hello,

first of all, thanks a lot for providing DSSR! It is one of the more useful secondary structure tools out there.

I ran into a problem with pseudoknots in the *.dbn output - higher-order pseudoknots are also assigned a '[]' pair instead of '{}' or some other bracket pair. This doesn't really limit the usefulness of DSSR, since I can bypass the problem by working with *.ct output, but it is confusing.

By the way, what algorithm do you use to identify which of the conflicting base pairs should be output as pseudoknots and which as "normal" base pairs?

Thanks & thumbs up!

--Jan Hajic, Charles University in Prague