The block spectrum of RNA pseudoknot structures

Abstract: In this paper we analyze the length-spectrum of blocks in $\gamma$-structures. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time RNA folding. A $\gamma$-structure is constructed by nesting and concatenating specific building components having topological genus at most $\gamma$. A block is a substructure enclosed by crossing maximal arcs with respect to the partial order induced by nesting. We show that, in uniformly generated $\gamma$-structures, there is a significant gap in this length-spectrum, i.e., there asymptotically almost surely exists a unique longest block of length at least $n-O(n^{1/2})$ and that with high probability any other block has finite length. For fixed $\gamma$, we prove that the length of the longest block converges to a discrete limit law, and that the distribution of short blocks of given length tends to a negative binomial distribution in the limit of long sequences. We refine this analysis to the length spectrum of blocks of specific pseudoknot types, such as H-type and kissing hairpins. Our results generalize the rainbow spectrum on secondary structures by the first and third authors and are being put into context with the structural prediction of long non-coding RNAs.