A new distance for high level RNA secondary structure comparison

TL;DR

This paper introduces a novel tree-based distance measure for comparing RNA secondary structures, incorporating new fusion operations to better identify common structural cores, with practical efficiency demonstrated on various RNAs.

Contribution

The paper proposes a new RNA structure comparison algorithm using node and edge fusion operations, improving over traditional tree edit methods.

Findings

Algorithm effectively compares RNA structures with new fusion operations.

Complexity depends only on successive fusions per node, not total fusions.

Demonstrated practical efficiency on ribosomal and other RNAs.

Abstract

We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling classically used in the literature. This allows us to address some serious limitations of the more traditional tree edit operations when the trees represent RNAs and what is searched for is a common structural core of two RNAs. Although the algorithm complexity has an exponential term, this term depends only on the number of successive fusions that may be applied to a same node, not on the total number of fusions. The algorithm remains therefore efficient in practice and is used for illustrative purposes on ribosomal as well as on other types of RNAs.