Loop-loop interaction metrics on RNA secondary structures with pseudoknots

Many methods have been proposed in the literature to face the problem of RNA secondary structures comparison. From a biological point of view, most of these methods are satisfactory for the comparison of pseudoknot free secondary structures, whereas the problem of pseudoknotted motifs comparison has not been solved yet. In this paper, we propose loop-loop interaction metrics, a new measure able to compute the distance of two pseudoknotted secondary structures by comparing loops and their interactions. The new measure is defined for RNA molecules whose structural and biological information is represented as algebraic expressions of hairpin loops, so that each RNA secondary structure can be represented as a word, which describes the interactions among loops and uniquely defines the intersection set, the set of pairs of loops that cross. Hence, the interaction metrics is defined as the symmetric set difference applied to the intersection sets of molecules. To illustrate how to apply the proposed methodology, we compare two RNA molecules, PKB66 and PKB10, extracted from Pseudobase++ database. To test the validity of the measure, we evaluated the evolutionary conservation of the pseudoknot domain of Vertebrate Telomerase RNA. Copyright © 2018 by SCITEPRESS – Science and Technology Publications, Lda. All rights reserved.