Question: Python-friendly tools for RNA secondary structure visualisation & manipulation
1
gravatar for Leszek
3.7 years ago by
Leszek4.0k
IIMCB, Poland
Leszek4.0k wrote:

I'm looking for Python tools (or tools with Python bindings) for manipulation and visualisation of RNA secondary structures. In principle, I would like to annotate (maybe with colours) some of the bases from 2D structures.  

Can you recommend me some solutions?  

ADD COMMENTlink modified 3.7 years ago by Ryan Dale4.8k • written 3.7 years ago by Leszek4.0k
2
gravatar for Ryan Dale
3.7 years ago by
Ryan Dale4.8k
Bethesda, MD
Ryan Dale4.8k wrote:

forgi is a Python package that allows a lot of flexibility in working with secondary structures. I've found it very useful; also see another answer (https://www.biostars.org/p/133492/#133555) for hints on loading from FASTA.

ADD COMMENTlink written 3.7 years ago by Ryan Dale4.8k

Thanks Ryan, that's really good hint! Actually I've found it in meantime :) I cannot find the option to generate the structure images, but I'll do some stats with forgi at least :D

ADD REPLYlink written 3.7 years ago by Leszek4.0k
0
gravatar for Asaf
3.7 years ago by
Asaf5.6k
Israel
Asaf5.6k wrote:

It's not a tool but rather a far starting point for what you're asking. The Vienna package has a script called colorrna.pl which is a small perl script that color the ss.ps file using the dp.ps file (base-pairing probabilities). You can take a look and see how they change the postscript file and enter colors as you will.

 

ADD COMMENTlink written 3.7 years ago by Asaf5.6k
0
gravatar for jsgounot
3.7 years ago by
jsgounot130
European Union
jsgounot130 wrote:

Maybe this lib : https://github.com/fjossinet/RNA-Science-Toolbox

ADD COMMENTlink written 3.7 years ago by jsgounot130
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