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Poster abstract: RNA thermodynamic conformational entropy by Juan-Antonio Garcia Martin; Peter Clote is a scholarly article available to read on EtoBox.

What is Poster abstract: RNA thermodynamic conformational entropy about?

We describe the first two accurate, cubic-time algorithms to compute the conformational entropy -kB s p(s) ln p(s) for RNA secondary structures s, with respect to the Turner energy model, where free energy parameters are determined from UV aborption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy values are much smaller than derivational entropy values, and the correlation between length-normalized thermodynamic entropy values and derivational entropy values is moderately weak to poor. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. Applying our algorithm to the HIV-1 genome indicates that certain

Author

Juan-Antonio Garcia Martin; Peter Clote

Publisher

ACM

Published

2015

Language

EN