Python-friendly tools for RNA secondary structure visualisation & manipulation
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6.1 years ago
Leszek 4.1k

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?  

python secondary structure RNA visualisation • 4.8k views
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6.1 years ago
Ryan Dale 4.9k

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 for hints on loading from FASTA.

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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

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6.1 years ago
Asaf 8.6k

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.

 

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6.1 years ago
jsgounot ▴ 140

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

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