Messages

1

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

« on: November 02, 2014, 10:21:39 am »

AFAIK, it's working all right. Thanks for the fix!

JH.

2

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

3

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

« on: May 11, 2014, 06:59:34 pm »

Well, I did find something by the group that started working on the Bio.RNA branch of Biopython, but I only skimmed it:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248259/

Not sure if it really is a must-read.

I came up with coloring a conflict graph (most such conflict graphs - at least so I thought - would be bipartite, with a comparatively small number of edges, where several long-range pseudoknot helices would be responsible for most edges). The greedy criterion for selecting the next component to color is simply the number of conflicting helices: I sort components by their highest degree vertex from highest to lowest and start coloring each one from this highest degree vertex, using a standard FIFO queue. The first color used is '[' (the helix with most conflicts of the component gets labeled as a pseudoknotted helix) and further colors are assigned based on a priority list that starts with '(', so that if currently possible, the helix should be a non-pseudoknotted helix. If the graph component is trivial (a helix with no conflicts), I start coloring it with '('.  There could be other greedy criteria - for instance some function of helix length, number of base pairs, number of spanned helices, etc.

JH.

4

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