Pseudoknot RNA Structures with Arc-Length $\ge 3$

Details Pseudoknot RNA Structures with Arc-Length $\ge 3$ Pseudoknot RNA Structures with Arc-Length $\ge 3$

2007-08-23

arxiv.org/abs/0708.3134v1

Mathematics

Combinatorics

18 pages, 4 figures

Scientific paper

In this paper we study $k$-noncrossing RNA structures with arc-length $\ge 3$, i.e. RNA molecules in which for any $i$, the nucleotides labeled $i$ and $i+j$ ($j=1,2$) cannot form a bond and in which there are at most $k-1$ mutually crossing arcs. Let ${\sf S}_{k,3}(n)$ denote their number. Based on a novel functional equation for the generating function $\sum_{n\ge 0}{\sf S}_{k,3}(n)z^n$, we derive for arbitrary $k\ge 3$ exponential growth factors and for $k=3$ the subexponential factor. Our main result is the derivation of the formula ${\sf S}_{3,3}(n) \sim \frac{6.11170\cdot 4!}{n(n-1)...(n-4)} 4.54920^n$.

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