A new entropy model for RNA: part IV, The Minimum Free Energy (mFE) and the thermodynamically most-probable folding pathway (TMPFP)

  • Wayne Dawson | dawson@bi.a.u-tokyo.ac.jp Bioinformation Engineering Laboratory, Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Japan.
  • Gota Kawai Chiba Institute of Technology, Japan.

Abstract

Here we discuss four important questions (1) how can we be sure that the thermodynamically most-probable folding-pathway yields the minimum free energy for secondary structure using the dynamic programming algorithm (DPA) approach, (2) what are its limitations, (3) how can we extend the DPA to find the minimum free energy with pseudoknots, and finally (4) what limitations can we expect to find in a DPA approach for pseudoknots. It is our supposition that some structures cannot be fit uniquely by the DPA, but may exist in real biology situations when disordered regions in the biomolecule are necessary. These regions would be identifiable by using suboptimal structure analysis. This grants us some qualitative tools to identify truly random RNA sequences, because such are likely to have greater degeneracy in their thermodynamically most-probable folding-pathway.

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Published
2015-07-13
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Section
Early Release
Keywords:
RNA folding, Entropy, Dynamic programming algorithm, RNA structure, functional RNA, bioinformatics
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  • Supplement S2: Methods: the vsfold5 algorithm: 0
  • Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding: 0
How to Cite
Dawson, W., & Kawai, G. (2015). A new entropy model for RNA: part IV, The Minimum Free Energy (mFE) and the thermodynamically most-probable folding pathway (TMPFP). Journal of Nucleic Acids Investigation, 5(1). https://doi.org/10.4081/jnai.2015.2653