Question: Calculating per base shannon entropy of predicted RNA Structures.
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gravatar for shreygandhi1990
4 weeks ago by
United States
shreygandhi19900 wrote:

I want to look for regions in my lncRNA sequences which are predicted to form stable structures. Is there any tool that can predict the Shannon entropy of predicted RNA secondary structures? This would enable me to look for highly structured regions in my RNA sequences.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by shreygandhi19900

Why are you interested in Shannon Entroy specifically? There are several tools to calculate RNA structure and to compute the probability of a nucleotide to be single stranded. See RNAfold from the Vienna package for instance, it computes the ensemble of structures and each nucleotide is assigned such a probability. http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi

ADD REPLYlink written 4 weeks ago by Asaf6.5k

Shannon entropy is not necessarily a good measure of structural stability. Do as Asaf says and run folding tools like RNAfold or ViennaRNA and do it more directly.

ADD REPLYlink written 4 weeks ago by Joe15k

My aim is to look at lincRNAs that have similar structures. Now as the accuracy of these structure predictions is not so good and will also influence the downstream alignment of lincRNA structures as well.

I read that Shannon entropy can enable me to check for stretches of RNA which have a high probability to form a stable structure. Thus, based on Shannon entropy, I wanted to shortlist structures beforehand which show stable structures and run this analysis for only such lncRNAs.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by shreygandhi19900

I can't understand what you will be computing the SE on, are you talking about conservation or RNA structure?

ADD REPLYlink written 4 weeks ago by Asaf6.5k

Yes, I have 10 human lncRNA sequences which show no sequence conservation across the other species. So, I decided to look for their conservation of RNA structure across species...

But since the structure prediction methods are not so accurate, I was thinking maybe out of these 10 lncRNAs, I will look for stretches which have a probability to form just 1 stable structure (by measuring this with low Shannon Entropy). And then do structural alignment (using a tool called BEAGLE) to look for structural homologs based on these stretches of lncRNAs as these might be important.

ADD REPLYlink written 4 weeks ago by shreygandhi19900

Something like that: https://github.com/debbiemarkslab/plmc ?

ADD REPLYlink written 4 weeks ago by Asaf6.5k

No not really.. I want to do something like this: https://www.mdpi.com/1422-0067/20/19/4770/htm But with predicted lncRNA structures.

ADD REPLYlink written 4 weeks ago by shreygandhi19900

Again, I'm a bit confused. Are you referring to information theory entropy or physical entropy? If you are looking for structures that are formed with high probability you can use RNAfold which compute an ensemble of structures and give the probability or entropy for each position.

ADD REPLYlink written 4 weeks ago by Asaf6.5k
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