Endhered patterns in matchings and RNA

TL;DR

This paper investigates the distribution and asymptotic behavior of endhered patterns in matchings and RNA structures, revealing differences between theoretical models and real-world RNA configurations.

Contribution

It introduces combinatorial analysis of endhered patterns in matchings and RNA, highlighting distribution differences and effects of transformations like endhered twist.

Findings

Patterns 21 and 12 are equidistributed in matchings but differ in native RNAs.

Distribution of size 3 endhered patterns varies under endhered twist.

Distributions of patterns in native RNA structures are computed and analyzed.

Abstract

An endhered (end-adhered) pattern is a subset of arcs in matchings, such that the corresponding starting points are consecutive and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations. We focus on the occurrence frequency of such patterns in matchings and native (real-world) RNA structures with pseudoknots. We present combinatorial results related to the distribution and asymptotic behavior of the pattern 21, which corresponds to two consecutive base pairs frequently encountered in RNA, and the pattern 12, representing the archetypal minimal pseudoknot. We show that in matchings these two patterns are equidistributed, which is quite different from what we can find in native RNAs. We also examine the distribution of endhered patterns of size 3, showing how the patterns change under the transformation called endhered twist. Finally, we compute the distributions of endhered patterns of size 2 and 3 in native secondary RNA structures with pseudoknots and discuss possible outcomes of our study.