Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots

TL;DR

This paper introduces a unified tree decomposition framework for RNA structure-sequence alignment, enabling efficient algorithms that handle complex features like tertiary interactions and pseudoknots, generalizing previous specialized methods.

Contribution

It presents a general parameterized algorithm for RNA structure-sequence alignment using tree decomposition, unifying and extending prior specific algorithms.

Findings

Algorithm complexity matches previous specialized methods

Framework handles complex RNA features like pseudoknots

Generalizes structure-sequence comparison approaches

Abstract

We present a general setting for structure-sequence comparison in a large class of RNA structures that unifies and generalizes a number of recent works on specific families on structures. Our approach is based on tree decomposition of structures and gives rises to a general parameterized algorithm, where the exponential part of the complexity depends on the family of structures. For each of the previously studied families, our algorithm has the same complexity as the specific algorithm that had been given before.