NDLI: Poster abstract: RNA thermodynamic conformational entropy

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Poster abstract: RNA thermodynamic conformational entropy

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Poster abstract: RNA thermodynamic conformational entropy

Content Provider	ACM Digital Library
Author	Garcia Martin, Juan-Antonio Clote, Peter
Abstract	We describe the first two accurate, cubic-time algorithms to compute the conformational entropy $--k_{B}$ $Σ_{s}$ p (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 genomic regions that harbor important secondary structures have low entropy, when compared to random (dinucleotide shuffled) RNA. This is the case with the --1 frameshift stimulating signal in the gag-pol overlap region. As well, by accounting for change of conformational entropy between the the bound and unbound hybridization complex of hammerhead ribozymes and their mRNA cleavage target, we show an improvement in predicting the hammerhead enzymatic activity (data not shown in this abstract). RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Upon publication of the journal article, the software will be made available at our web site.
Starting Page	482
Ending Page	483
Page Count	2
File Format	PDF
ISBN	9781450338530
DOI	10.1145/2808719.2811418
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2015-09-09
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Hiv-1 Ribozyme Entropy Rna secondary structure
Content Type	Text
Resource Type	Article

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