Irreducibility in RNA structures

Details Irreducibility in RNA structures Irreducibility in RNA structures

2009-02-22

arxiv.org/abs/0902.3784v1

Biology

Quantitative Biology

Biomolecules

17 figures 28 pages

Scientific paper

In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various distributions: of the numbers of irreducible substructures, their locations and sizes, parameterized in terms of the maximal number of mutually crossing arcs, $k-1$, and the minimal size of stacks $\sigma$. In particular, we analyze the size of the largest irreducible substructure for random and mfe structures, which is the key factor for the folding time of mfe configurations.

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