Pattern Matching and Local Alignment for RNA Structures

TL;DR

This paper introduces algorithms for pattern matching and local alignment of RNA structures, enabling better comparison of RNA secondary structures with exact and approximate matching capabilities.

Contribution

It presents novel algorithms for exact and approximate pattern matching and local structural alignment of RNA, addressing limitations of previous methods.

Findings

Algorithms for exact RNA structure pattern matching

Algorithms for approximate RNA structure pattern matching

Algorithm for RNA local structural alignment

Abstract

The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between A-U and G-C. For secondary structures, these bonds have been traditionally assumed to be one-to-one and non-crossing. This paper considers pattern matching as well as local alignment between two RNA structures. For pattern matching, we present two algorithms, one for obtaining an exact match, the other for approximate match. We then present an algorithm for RNA local structural alignment.